Contacts of the strand formed by residues 785 - 793 (chain D) in PDB entry 3N1G
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 SER 785 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A ASN* 3.8 17.5 + - - -
181A HIS* 5.9 1.7 + - - -
754D PRO* 3.6 6.6 - - - +
755D THR* 2.6 49.5 + - - +
756D ASP 4.8 0.2 + - - -
784D THR* 1.3 78.8 - - - +
786D TYR* 1.3 57.7 + - - +
806D ILE* 3.2 21.5 - - - +
807D CYS 3.6 5.4 + - - -
808D GLU* 3.6 21.0 - - - +
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Residues in contact with TYR 786 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729D ILE* 4.0 18.2 - - + -
752D TYR* 4.6 8.3 - + + -
753D ARG 3.3 24.2 - - - +
754D PRO* 3.8 22.6 - - + +
755D THR* 3.3 6.2 + - - -
777D ILE* 6.3 0.2 - - + -
780D LEU* 3.5 37.2 - - + +
781D GLN* 2.9 34.1 + - - +
784D THR* 3.3 35.6 - - + +
785D SER* 1.3 72.3 + - - +
787D ASP* 1.3 60.2 + - - +
788D ILE* 3.9 15.5 + - + +
805D MET 3.6 0.5 - - - +
806D ILE* 3.2 5.9 - - - -
807D CYS 2.8 36.8 + - - +
809D THR* 4.0 4.3 - - + -
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Residues in contact with ASP 787 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LYS* 2.7 37.2 + - - -
90A GLU* 4.5 4.7 - - - -
752D TYR* 3.1 6.6 - - - -
753D ARG* 2.7 52.5 + - - +
755D THR* 2.9 29.0 + - - +
757D SER 3.8 0.5 - - - +
763D TYR* 3.7 21.1 - - + +
786D TYR* 1.3 71.8 - - - +
788D ILE* 1.3 61.5 + - - +
804D VAL* 4.5 5.2 - - + -
805D MET 3.5 5.4 - - - +
806D ILE* 4.0 7.0 - - - +
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Residues in contact with ILE 788 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718D ILE* 3.8 11.2 - - + +
721D THR* 4.7 8.3 - - + -
729D ILE* 3.8 35.7 - - + -
731D LEU* 4.4 14.4 - - + -
750D ILE* 4.4 8.1 - - + -
751D TYR 3.4 9.0 - - - +
752D TYR* 4.4 1.1 - - + -
777D ILE* 4.0 25.8 - - + -
786D TYR* 4.0 13.7 - - + +
787D ASP* 1.3 81.6 - - - +
789D LYS* 1.3 64.3 + - - +
804D VAL* 3.4 5.4 - - - +
805D MET* 2.8 45.5 + - + +
807D CYS* 4.2 17.9 - - + +
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Residues in contact with LYS 789 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLU 4.6 3.0 + - - -
92A ASN* 4.2 17.8 - - - +
718D ILE* 3.9 4.0 - - - -
750D ILE* 3.7 1.7 - - - +
751D TYR* 2.7 41.2 + - + +
760D ASP* 4.6 7.1 + - - +
763D TYR* 3.7 42.4 + - + +
788D ILE* 1.3 76.5 - - - +
790D MET* 1.3 64.1 + - - +
801D PHE* 3.6 51.4 - - + -
802D SER* 3.6 15.0 - - - +
803D ASN 3.8 5.6 - - - +
804D VAL* 4.0 19.3 - - + -
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Residues in contact with MET 790 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716D PRO* 3.7 11.9 - - + +
718D ILE* 3.8 13.0 - - + -
731D LEU* 4.2 4.9 - - - -
733D TRP* 3.3 63.7 - - + -
748D PHE* 3.7 31.9 - - + -
749D TYR 3.1 15.9 - - - +
750D ILE* 4.1 13.5 - - + -
751D TYR* 4.2 2.7 - - - -
789D LYS* 1.3 77.3 - - - +
791D GLN* 1.3 64.7 + - - +
801D PHE* 3.5 4.8 - - - -
802D SER* 2.8 45.0 + - - +
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Residues in contact with GLN 791 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716D PRO* 3.6 11.0 - - - -
748D PHE* 3.2 7.8 - - - +
749D TYR* 2.9 33.3 + - + +
751D TYR* 2.4 42.5 + - + -
790D MET* 1.3 74.3 - - - +
792D CYS* 1.3 64.7 + - - +
798D GLU* 3.3 27.3 - - + +
799D SER* 3.1 32.8 + - - +
800D GLU 3.8 4.0 - - - +
801D PHE* 3.3 25.7 - - - -
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Residues in contact with CYS 792 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712D PRO* 3.7 12.1 - - - -
714D ALA 3.9 0.7 - - - -
715D GLY* 4.6 1.3 - - - -
716D PRO* 3.7 2.1 - - + +
735D TYR* 3.5 35.0 - - - -
745D ILE* 4.1 9.2 - - + -
747D GLY 3.4 12.8 - - - +
748D PHE* 3.7 21.1 - - + -
791D GLN* 1.3 78.1 - - - +
793D PHE* 1.3 65.0 + - - +
798D GLU* 3.5 2.1 - - - +
799D SER* 2.9 48.6 + - - -
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Residues in contact with PHE 793 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712D PRO* 4.1 4.0 - - - -
745D ILE* 3.4 4.4 - - - +
746D HIS* 2.7 54.8 + + + -
747D GLY* 3.0 46.8 + - - -
748D PHE 3.5 9.4 - - - -
749D TYR* 3.5 59.2 - + + -
767D MET* 3.9 15.0 - - + -
792D CYS* 1.3 79.2 - - - +
794D ASN* 1.3 65.8 + - - +
797D GLY 3.2 14.8 - - - +
798D GLU* 3.9 7.4 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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