Contacts of the helix formed by residues 768 - 787 (chain J) in PDB entry 6PSU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 768 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618I GLN* 5.9 3.9 - - + +
620I ASN* 4.1 37.4 + - + +
1187I PHE* 4.6 6.7 - - - -
766J GLY 4.3 0.4 - - - -
767J LEU* 1.3 77.0 - - - +
769J VAL* 1.3 67.9 + - + +
770J LEU* 3.8 6.1 + - - +
771J GLN* 2.5 63.1 + - - +
772J TYR* 3.0 6.9 + - - +
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Residues in contact with VAL 769 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555I TYR* 3.0 18.1 - - - +
618I GLN* 3.0 33.2 - - + +
619I ALA* 6.0 2.0 - - + -
620I ASN* 5.3 4.9 - - + +
657I THR* 3.5 28.3 - - - +
660I VAL* 3.5 15.9 - - + +
1187I PHE* 3.4 33.9 - - + -
768J ASN* 1.3 74.0 - - + +
770J LEU* 1.3 61.3 + - + +
772J TYR* 3.5 2.9 + - - +
773J PHE* 2.9 29.5 + - - +
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Residues in contact with LEU 770 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555I TYR* 3.5 30.5 - - + +
618I GLN* 3.1 34.3 - - + +
635I THR* 6.4 1.8 - - - -
636I CYS 5.4 0.2 - - - -
637I ARG* 3.9 18.8 - - + +
642I SER* 3.6 33.2 - - - +
768J ASN* 3.2 5.8 + - - +
769J VAL* 1.3 74.3 - - - +
771J GLN* 1.3 62.3 + - + +
773J PHE* 3.8 5.3 - - + +
774J ILE* 2.9 44.1 + - + +
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Residues in contact with GLN 771 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758J PRO 5.4 1.8 - - - +
759J ILE* 3.3 35.7 - - + +
760J THR* 4.2 10.3 + - - +
761J ALA* 3.5 33.2 - - - +
766J GLY 4.2 0.2 - - - +
767J LEU* 3.1 14.5 - - + -
768J ASN* 2.5 59.4 + - - +
770J LEU* 1.3 78.2 - - - +
772J TYR* 1.3 62.3 + - - +
774J ILE* 3.3 2.7 + - + +
775J SER* 3.0 21.8 + - - -
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Residues in contact with TYR 772 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560I PRO* 6.4 0.4 - - + -
561I ILE* 3.6 26.9 - - + -
660I VAL* 6.3 0.4 - - + -
661I VAL* 6.2 1.6 - - + -
671I LEU* 3.6 24.5 - - + +
672I GLU 4.5 3.1 - - - -
674I ASP 3.0 28.9 + - - -
675I ASP 3.2 14.0 + - - -
676I ALA* 3.3 17.7 - - + -
679I ALA* 3.4 14.0 - - - +
1187I PHE* 3.8 34.1 - + + -
744J ARG* 6.2 0.2 - - - -
763J PHE* 5.0 2.5 - + - -
767J LEU* 4.3 18.7 - - + +
768J ASN 3.0 9.5 + - - +
769J VAL 3.9 4.9 - - - +
771J GLN* 1.3 76.7 - - - +
773J PHE* 1.3 63.1 + - - +
775J SER* 3.0 10.6 + - - -
776J THR* 2.8 29.7 + - - -
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Residues in contact with PHE 773 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550I VAL* 4.5 8.5 - - + -
551I HIS 4.0 10.8 - - - -
552I PRO* 4.1 20.0 - - + -
554I HIS* 4.0 7.4 - - + -
555I TYR* 3.7 48.2 - + + -
560I PRO* 3.5 25.8 - - + -
660I VAL* 3.4 22.2 - - + -
769J VAL 2.9 17.6 + - - +
770J LEU* 3.8 8.7 - - + +
771J GLN 3.3 0.2 - - - -
772J TYR* 1.3 77.0 - - - +
774J ILE* 1.3 59.9 - - + +
776J THR* 2.9 26.6 + - - -
777J HIS* 3.5 22.0 - - - -
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Residues in contact with ILE 774 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642I SER* 5.9 2.2 - - - +
746J LEU 4.4 3.1 - - - +
747J MET* 3.5 29.0 - - + +
755J ILE* 4.3 23.6 - - + -
757J THR* 4.3 21.8 - - - +
758J PRO 5.4 0.4 - - - +
759J ILE* 3.3 30.7 - - + -
770J LEU* 2.9 31.5 + - + +
771J GLN* 4.9 0.2 - - - -
773J PHE* 1.3 78.2 - - + +
775J SER* 1.3 61.9 + - - +
776J THR 3.4 0.3 + - - -
777J HIS* 3.7 21.7 + - + +
778J GLY 4.4 1.0 + - - -
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Residues in contact with SER 775 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675I ASP* 5.3 1.6 + - - -
676I ALA* 4.5 14.7 + - - +
744J ARG* 3.3 34.9 + - - -
747J MET* 4.1 14.9 - - - +
759J ILE* 5.7 0.7 - - - -
767J LEU* 5.2 1.8 - - - -
771J GLN 3.0 12.7 + - - -
772J TYR* 3.0 17.8 + - - -
774J ILE* 1.3 77.1 - - - +
776J THR* 1.3 63.7 + - - +
777J HIS 3.2 0.7 + - - -
778J GLY* 3.4 3.6 + - - -
779J ALA* 3.1 21.1 + - - +
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Residues in contact with THR 776 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550I VAL* 4.2 9.4 - - + -
560I PRO* 3.2 47.8 - - + +
561I ILE* 4.3 7.4 - - + +
676I ALA* 4.5 5.6 - - + -
772J TYR* 2.8 26.2 + - - -
773J PHE* 2.9 14.8 + - - -
775J SER* 1.3 76.5 - - - +
777J HIS* 1.3 65.5 + - - +
779J ALA* 4.3 5.6 - - - -
780J ARG* 2.9 27.9 + - + +
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Residues in contact with HIS 777 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550I VAL* 3.1 32.9 + - + +
551I HIS* 4.5 0.9 - - - -
552I PRO* 4.1 32.2 - - + +
748J ALA 4.3 7.6 - - - +
749J LYS* 4.3 13.0 + - - -
750J PRO* 3.9 32.6 - - + +
755J ILE* 4.3 14.9 - - + +
773J PHE* 3.5 34.7 + + - -
774J ILE* 3.7 18.2 - - - +
775J SER 3.2 0.6 - - - -
776J THR* 1.3 79.0 - - - +
778J GLY* 1.3 64.2 + - - +
780J ARG* 3.6 2.3 - - - +
781J LYS* 3.0 23.2 + - - +
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Residues in contact with GLY 778 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747J MET* 5.3 4.9 - - - -
748J ALA 4.1 13.5 + - - -
749J LYS 5.4 1.8 - - - -
750J PRO* 5.7 0.2 - - - -
774J ILE 4.4 1.4 + - - -
775J SER 3.4 5.1 + - - -
777J HIS* 1.3 76.9 - - - +
779J ALA* 1.3 62.5 + - - +
781J LYS* 4.0 4.4 - - - +
782J GLY 2.9 11.8 + - - -
12N THR* 2.6 40.6 + - - -
15N LEU* 5.7 4.3 - - - -
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Residues in contact with ALA 779 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675I ASP* 4.5 3.1 - - - +
676I ALA* 3.2 31.2 - - + -
677I ASN* 3.0 35.1 + - - +
747J MET* 5.8 0.2 - - - -
775J SER* 3.1 13.4 + - - +
776J THR* 4.0 2.2 - - + +
778J GLY* 1.3 75.1 - - - +
780J ARG* 1.3 63.9 + - - +
782J GLY* 3.9 0.3 - - - -
783J LEU* 3.0 20.6 + - - +
12N THR* 4.2 5.5 - - - +
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Residues in contact with ARG 780 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548I ARG 3.6 27.5 + - - +
549I ASP* 4.3 5.8 - - - +
550I VAL* 4.1 30.4 - - + +
560I PRO* 2.2 35.2 + - - +
561I ILE* 4.3 3.4 - - - +
563I THR* 3.6 23.0 + - - -
569I ILE* 3.7 22.2 - - - +
570I GLY* 4.5 2.4 - - - -
573I ASN* 4.0 16.8 + - - +
680I LEU* 4.4 11.3 - - - +
776J THR* 2.9 20.9 + - + +
777J HIS 3.6 2.9 - - - +
779J ALA* 1.3 78.7 - - - +
781J LYS* 1.3 60.5 + - - +
783J LEU* 3.4 4.0 + - - +
784J ALA* 2.9 30.1 + - + +
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Residues in contact with LYS 781 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545I PHE* 3.6 43.0 + - - +
549I ASP* 5.4 5.4 - - + +
750J PRO* 3.9 43.5 - - + +
751J ASP* 5.8 0.9 - - - +
777J HIS 3.0 17.3 + - - +
778J GLY* 4.0 3.8 - - - +
780J ARG* 1.3 79.7 - - + +
782J GLY* 1.3 63.2 + - - +
784J ALA* 3.1 7.2 + - + +
785J ASP* 3.0 46.8 + - - +
933J ARG* 5.0 9.7 - - - +
11N VAL* 6.0 1.3 - - + -
15N LEU* 4.5 13.0 - - + -
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Residues in contact with GLY 782 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778J GLY 2.9 10.9 + - - -
779J ALA 3.9 0.4 - - - -
781J LYS* 1.3 77.6 - - - +
783J LEU* 1.3 56.1 + - - +
785J ASP 3.7 0.5 - - - -
786J THR* 2.9 30.3 + - - +
8N ALA* 3.4 15.6 - - - +
11N VAL* 3.9 16.8 - - - +
12N THR* 3.4 20.3 + - - +
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Residues in contact with LEU 783 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565I GLU* 4.0 15.9 - - + -
566I GLY 4.1 3.8 - - - +
569I ILE* 3.2 23.1 - - + -
677I ASN* 3.9 22.4 - - + +
680I LEU* 3.9 38.6 - - + -
681I MET* 4.6 8.7 - - + -
779J ALA 3.0 17.6 + - - +
780J ARG* 4.0 3.8 - - - +
782J GLY* 1.3 76.6 - - - +
784J ALA* 1.3 61.1 + - - +
786J THR* 3.0 25.0 - - + +
787J ALA* 3.1 9.9 + - + +
4N GLU* 4.9 12.3 - - + +
5N ALA 5.5 0.2 - - - +
8N ALA* 3.4 8.5 - - + +
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Residues in contact with ALA 784 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545I PHE* 5.4 4.4 - - + -
548I ARG* 4.9 20.4 + - + +
569I ILE* 3.8 25.7 - - + +
780J ARG* 2.9 22.1 + - + +
781J LYS* 3.1 10.5 + - + +
783J LEU* 1.3 79.1 - - - +
785J ASP* 1.3 65.0 + - - +
787J ALA* 3.6 9.9 + - - +
788J LEU* 3.8 15.4 + - - +
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Residues in contact with ASP 785 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545I PHE* 3.8 27.5 - - - -
781J LYS* 3.0 43.9 + - - +
782J GLY 3.7 2.2 - - - +
784J ALA* 1.3 79.8 - - - +
786J THR* 1.3 62.8 + - - +
787J ALA 3.3 0.4 - - - -
788J LEU* 3.5 6.8 + - - +
789J LYS* 3.5 7.8 + - - +
932J MET* 3.0 36.8 - - + +
933J ARG* 4.4 19.3 + - + +
11N VAL* 4.4 17.5 - - + +
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Residues in contact with THR 786 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782J GLY 2.9 16.2 + - - +
783J LEU* 3.0 25.4 - - + +
785J ASP* 1.3 75.2 - - - +
787J ALA* 1.3 57.0 + - - +
788J LEU 3.1 7.5 + - - -
789J LYS* 4.0 14.0 + - - +
790J THR* 3.7 10.0 + - - -
4N GLU* 3.0 33.5 + - + +
7N GLU* 3.4 18.5 + - - +
8N ALA* 3.2 27.8 - - + -
11N VAL* 4.5 7.2 - - - +
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Residues in contact with ALA 787 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566I GLY* 3.1 48.4 - - - +
567I PRO* 5.4 1.6 - - - +
569I ILE* 4.6 1.8 - - + -
783J LEU* 3.1 18.4 + - + +
784J ALA 3.6 6.5 + - - +
785J ASP 3.3 0.6 - - - -
786J THR* 1.3 77.7 - - - +
788J LEU* 1.3 57.7 + - - +
790J THR* 4.2 15.5 - - - -
791J ALA* 4.5 3.8 + - - +
4N GLU* 5.4 5.4 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il