Contacts of the helix formed by residues 627 - 643 (chain A) in PDB entry 3F2B
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 627 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625A ALA* 3.4 2.5 - - - +
626A GLN* 1.3 87.3 - - - +
628A GLU* 1.3 61.9 + - + +
629A THR* 3.1 15.5 + - - -
630A GLY* 2.9 21.8 + - - -
631A LEU* 2.8 25.5 + - - +
662A ASP* 5.7 0.8 + - - -
663A GLY* 3.6 14.9 - - - -
812A GLY* 5.5 1.3 - - - -
814A VAL* 4.1 13.7 - - - +
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Residues in contact with GLU 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A ASN* 1.3 73.2 - - + +
629A THR* 1.3 67.3 + - - +
631A LEU* 3.6 14.8 - - + +
632A LYS* 2.9 30.0 + - - +
814A VAL* 4.8 6.8 - - + +
815A LYS 6.2 1.6 - - - +
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Residues in contact with THR 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A ASN* 3.1 13.4 + - - -
628A GLU* 1.3 83.9 + - - +
630A GLY* 1.3 64.4 + - - +
632A LYS* 3.2 5.9 + - - +
633A ASN* 2.9 31.6 + - - +
662A ASP* 3.8 33.0 - - + +
663A GLY* 4.8 1.1 - - - -
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Residues in contact with GLY 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A ALA* 3.7 6.3 - - - -
627A ASN* 2.9 14.5 + - - -
629A THR* 1.3 77.4 - - - +
631A LEU* 1.3 61.2 + - - +
633A ASN* 3.3 1.5 + - - -
634A LEU* 2.9 19.9 + - - +
662A ASP 3.6 5.8 + - - -
663A GLY 3.3 31.9 - - - -
664A LEU* 3.3 11.7 - - - +
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Residues in contact with LEU 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A PHE* 3.9 22.0 - - + -
402A TYR* 4.7 3.6 - - + -
625A ALA* 3.7 7.3 - - + +
627A ASN 2.8 16.4 + - - +
628A GLU* 3.7 16.2 - - + +
629A THR 3.2 0.2 - - - -
630A GLY* 1.3 71.8 - - - +
632A LYS* 1.3 65.7 + - + +
634A LEU* 3.0 17.1 + - + +
635A PHE* 3.0 47.0 + - + -
814A VAL* 4.3 16.6 - - + -
815A LYS 4.0 9.0 - - - +
816A PRO* 3.7 30.3 - - + +
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Residues in contact with LYS 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A GLU 2.9 17.5 + - - +
629A THR* 3.8 5.2 - - - +
631A LEU* 1.3 79.5 - - + +
633A ASN* 1.3 57.5 + - - +
635A PHE* 3.0 9.7 + - - +
636A LYS* 2.9 42.3 + - - +
1062A GLU* 2.7 30.0 + - - +
1064A TYR* 3.9 26.2 - - + +
1065A ASP* 2.5 32.5 + - - +
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Residues in contact with ASN 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PO4 4.2 4.6 + - - -
629A THR* 2.9 23.4 + - - +
630A GLY 3.7 3.8 - - - +
632A LYS* 1.3 76.7 - - - +
634A LEU* 1.3 57.2 + - - +
636A LYS* 3.7 13.1 - - - +
637A LEU* 2.9 36.3 + - - +
659A LYS 5.0 0.4 + - - -
660A HIS* 3.1 55.1 - - - +
662A ASP* 3.0 27.0 + - - +
664A LEU* 4.3 3.1 - - + -
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Residues in contact with LEU 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL* 4.5 6.3 - - + -
386A PHE* 4.1 13.2 - - + -
402A TYR 3.7 23.3 - - - +
403A GLY* 3.9 19.3 - - - +
404A LEU* 4.0 27.5 - - + +
623A LEU* 4.0 14.1 - - + -
625A ALA* 4.1 8.3 - - + +
630A GLY 2.9 16.0 + - - +
631A LEU* 3.0 10.3 + - - +
633A ASN* 1.3 76.2 - - - +
635A PHE* 1.3 57.8 + - + +
637A LEU* 3.4 3.1 + - + +
638A VAL* 2.6 40.8 + - + +
664A LEU* 3.8 19.3 - - + -
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Residues in contact with PHE 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL* 4.1 5.8 - - + -
386A PHE* 4.1 11.7 - + - -
631A LEU* 3.0 46.1 + - + -
632A LYS* 3.0 10.1 + - - +
634A LEU* 1.3 79.6 - - + +
636A LYS* 1.3 61.6 + - - +
639A SER* 2.8 29.2 + - - -
816A PRO 3.9 13.2 - - - -
1064A TYR* 3.5 29.4 - - + +
1065A ASP 5.1 2.0 - - - -
1066A PHE* 3.7 22.9 - - - -
1067A THR* 3.8 7.9 - - - -
1068A PRO* 3.5 31.0 - - + +
1085A PHE* 3.6 28.3 - + - -
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Residues in contact with LYS 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PO4 2.6 43.5 + - - +
632A LYS* 2.9 35.8 + - + +
633A ASN* 3.7 21.6 - - - +
634A LEU 3.2 0.2 - - - -
635A PHE* 1.3 76.8 - - - +
637A LEU* 1.3 53.0 + - - +
639A SER* 3.1 8.4 + - - -
640A LEU* 2.8 42.6 + - + +
660A HIS* 4.0 14.8 - - + +
1062A GLU* 4.3 12.4 + - - -
1064A TYR* 4.0 29.2 - - + -
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Residues in contact with LEU 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LEU* 4.6 6.3 - - + -
623A LEU* 4.4 7.4 - - + -
633A ASN 2.9 24.0 + - - +
634A LEU* 3.7 7.0 - - - +
636A LYS* 1.3 68.9 - - - +
638A VAL* 1.3 65.2 + - - +
640A LEU* 4.0 3.2 - - + +
641A SER* 2.9 28.5 + - - -
652A ILE* 3.8 38.4 - - + +
656A VAL* 3.9 14.4 - - + +
657A LEU* 4.2 12.3 - - + -
660A HIS* 3.7 46.7 - - + +
664A LEU* 4.1 14.8 - - + -
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Residues in contact with VAL 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ALA 4.1 12.6 - - - +
382A VAL* 5.1 0.2 - - - -
383A VAL* 4.1 18.4 - - + -
404A LEU* 4.7 9.6 - - + +
634A LEU 2.6 30.0 + - - +
635A PHE* 3.8 7.9 - - - +
637A LEU* 1.3 75.1 - - - +
639A SER* 1.3 61.5 - - - +
641A SER* 3.1 9.5 + - - -
642A HIS* 2.8 32.8 + - + +
1068A PRO* 3.5 24.2 - - + -
1069A ILE 4.7 1.8 - - - +
1084A HIS* 3.8 29.6 - - + +
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Residues in contact with SER 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635A PHE 2.8 18.1 + - - -
636A LYS 3.1 9.2 + - - -
638A VAL* 1.3 78.1 - - - +
640A LEU* 1.3 65.3 + - - +
642A HIS* 3.1 2.4 + - - -
643A ILE* 3.0 30.5 + - - +
644A GLN* 4.9 0.7 - - - -
1064A TYR* 3.3 21.7 - - - -
1068A PRO* 3.4 0.5 - - - +
1069A ILE* 2.9 46.1 + - - -
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Residues in contact with LEU 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A PO4 5.7 0.2 - - - +
636A LYS* 2.8 25.4 + - + +
637A LEU* 4.1 4.7 - - + +
639A SER* 1.3 75.3 - - - +
641A SER* 1.3 60.2 + - - +
644A GLN* 3.2 39.8 + - + +
645A TYR* 2.9 44.9 + - + +
652A ILE* 6.3 1.1 - - + -
656A VAL* 3.8 16.8 - - + -
660A HIS* 3.5 33.9 - - + +
1064A TYR* 6.1 0.9 - - - +
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Residues in contact with SER 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A ALA* 4.7 2.1 + - - +
637A LEU 2.9 16.9 + - - -
638A VAL* 3.1 18.2 + - - +
640A LEU* 1.3 77.7 - - - +
642A HIS* 1.3 66.1 + - - +
645A TYR* 4.4 0.4 - - - -
646A PHE* 3.4 13.2 - - - -
650A PRO* 3.2 26.7 - - - +
651A ARG 3.4 33.8 + - - -
652A ILE* 3.7 14.9 - - - +
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Residues in contact with HIS 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A ALA 3.2 26.7 - - - -
382A VAL* 4.2 13.7 - - + +
638A VAL* 2.8 33.2 + - + +
639A SER 3.1 4.3 + - - +
640A LEU 3.1 0.6 - - - -
641A SER* 1.3 86.1 + - - +
643A ILE* 1.3 63.2 + - - +
646A PHE* 3.5 20.1 - + - +
650A PRO* 3.7 25.8 - - + +
1069A ILE 4.8 0.2 - - - -
1070A GLN* 3.6 37.0 + - + -
1071A TYR* 3.8 15.2 + - - +
1074A ASP* 3.5 27.6 + - - +
1076A THR* 4.9 0.2 - - - +
1084A HIS* 4.4 1.1 - + - -
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Residues in contact with ILE 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639A SER 3.0 12.0 + - - +
640A LEU 3.2 0.4 + - - -
642A HIS* 1.3 84.4 - - - +
644A GLN* 1.3 87.2 + - + +
645A TYR 3.3 0.6 + - - -
646A PHE* 3.9 8.5 + - - +
1069A ILE* 3.6 32.8 - - + -
1070A GLN* 3.8 22.0 - - - +
1071A TYR* 3.7 34.1 - - + +
1076A THR* 4.6 5.7 - - - +
1081A ARG* 3.8 25.6 - - + -
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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
------------------------------------------------------------
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