Contacts of the helix formed by residues 620 - 631 (chain S) in PDB entry 1NVU
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 ASP 620 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37Q GLU* 4.2 3.7 + - - -
598S ILE* 3.1 27.8 - - + +
599S PRO 5.0 3.1 - - - +
618S TYR* 4.3 9.4 + - + -
619S ALA* 1.3 77.5 - - - +
621S PRO* 1.3 62.3 - - - +
622S ASN* 2.9 28.7 - - - +
623S PHE* 2.8 48.2 + - + +
624S VAL* 3.5 7.2 + - - +
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Residues in contact with PRO 621 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Q GLU* 4.2 27.8 - - + +
38Q ASP* 4.3 1.8 - - - -
39Q SER* 3.5 28.5 - - - +
56Q LEU* 3.8 29.6 - - + -
619S ALA* 4.0 6.5 - - + -
620S ASP* 1.3 87.4 - - - +
622S ASN* 1.3 62.6 + - - +
624S VAL* 3.3 14.3 + - + +
625S ARG* 3.2 22.0 + - - +
691S ASN* 5.9 0.7 - - - +
695S HIS* 6.2 2.5 - - + -
1047S PO4 4.7 1.2 + - - -
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Residues in contact with ASN 622 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Q SER* 5.0 5.5 + - - +
41Q ARG* 5.1 9.2 + - - -
620S ASP* 2.9 16.3 + - - +
621S PRO* 1.3 79.0 - - + +
623S PHE* 1.3 61.7 + - - +
625S ARG* 3.5 29.0 + - - +
626S THR* 3.0 35.5 + - - -
962S ARG* 5.9 5.3 - - - +
966S GLU* 5.5 4.2 + - - +
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Residues in contact with PHE 623 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601S ILE* 3.4 35.0 - - + -
609S LEU* 3.7 20.0 - - + -
612S ARG* 4.4 6.1 - - + +
613S LEU* 3.5 44.6 - - + +
620S ASP* 2.8 33.0 + - + +
622S ASN* 1.3 80.4 - - - +
624S VAL* 1.3 57.4 + - + +
626S THR* 3.2 5.4 + - - -
627S PHE* 2.8 39.9 + + - +
958S PHE* 3.6 35.2 - + - -
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Residues in contact with VAL 624 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Q GLU* 5.7 3.1 - - - +
613S LEU* 3.8 28.3 - - + +
620S ASP 4.1 10.1 - - - +
621S PRO* 3.3 13.7 + - + +
622S ASN 3.3 0.4 - - - -
623S PHE* 1.3 76.8 - - + +
625S ARG* 1.3 58.9 + - - +
627S PHE* 4.0 0.2 - - - +
628S LEU* 2.9 47.5 + - + +
688S ARG 6.0 0.2 - - - +
691S ASN* 4.6 12.6 - - - +
692S VAL* 4.6 16.6 - - + -
695S HIS* 4.2 18.2 - - + +
1047S PO4 3.9 10.8 - - - +
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Residues in contact with ARG 625 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621S PRO 3.2 12.2 + - - +
622S ASN* 3.6 29.8 + - - +
624S VAL* 1.3 78.6 - - - +
626S THR* 1.3 64.5 + - - +
628S LEU* 3.9 0.5 - - - +
629S THR* 2.7 39.6 + - - +
700S HIS* 5.7 0.2 - - + -
965S ALA* 2.8 40.0 + - - +
966S GLU* 4.8 3.8 - - - +
968S THR* 3.7 9.1 + - - -
969S GLY* 3.6 19.2 - - - -
972S GLN* 3.9 16.8 + - - +
1047S PO4 3.3 40.3 + - - +
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Residues in contact with THR 626 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622S ASN* 3.0 27.4 + - - -
623S PHE* 3.6 6.1 - - - -
625S ARG* 1.3 81.2 + - - +
627S PHE* 1.3 57.1 + - - +
629S THR* 3.3 0.3 + - - -
630S THR* 2.8 36.6 + - - +
958S PHE* 3.7 24.0 - - + -
961S ARG 3.8 14.8 - - - +
962S ARG* 3.9 15.4 + - + +
965S ALA* 3.5 32.9 - - + +
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Residues in contact with PHE 627 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606S VAL* 5.6 1.1 - - + -
609S LEU* 4.2 17.0 - - + -
610S ILE* 4.1 21.8 - - + -
613S LEU* 3.8 26.9 - - + -
623S PHE* 2.8 38.1 + + + +
624S VAL 4.0 2.2 - - - +
626S THR* 1.3 74.6 - - - +
628S LEU* 1.3 66.7 + - + +
629S THR 3.1 0.2 + - - -
630S THR* 3.1 4.2 + - - -
631S TYR* 2.8 54.7 + + + +
634S PHE* 3.8 28.3 - + - -
635S CYS* 5.5 2.7 - - + -
640S LEU* 3.9 27.8 - - + -
958S PHE* 4.4 10.3 - + + -
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Residues in contact with LEU 628 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613S LEU* 5.8 0.7 - - + -
624S VAL* 2.9 28.7 + - + +
625S ARG 4.1 0.4 - - - +
627S PHE* 1.3 88.2 - - + +
629S THR* 1.3 57.4 + - - +
631S TYR* 3.6 4.8 - - + -
632S ARG* 3.0 31.4 + - - -
640S LEU* 4.4 11.9 - - + -
692S VAL* 3.9 19.1 - - + +
695S HIS* 3.7 18.4 - - + -
696S TRP* 3.5 52.3 - - + +
700S HIS* 3.6 23.0 + - + +
1047S PO4 4.7 1.3 - - - +
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Residues in contact with THR 629 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625S ARG* 2.7 32.9 + - - +
626S THR* 3.6 5.4 - - - -
628S LEU* 1.3 79.2 - - - +
630S THR* 1.3 64.2 + - + +
632S ARG* 3.4 12.6 + - - +
700S HIS* 3.6 17.1 - - - -
702S TYR* 5.1 0.7 + - - -
801S PRO* 4.1 20.9 - - + +
805S VAL* 3.6 33.4 - - + +
965S ALA* 5.1 2.7 - - + -
968S THR* 4.2 16.6 + - + +
972S GLN* 5.4 1.4 + - - -
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Residues in contact with THR 630 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626S THR* 2.8 22.2 + - - +
627S PHE* 3.9 2.6 + - - -
629S THR* 1.3 93.6 - - + +
631S TYR* 1.3 64.8 + - - +
632S ARG* 3.2 5.0 + - - -
633S SER* 3.3 19.4 + - - -
634S PHE* 3.8 5.3 - - - -
805S VAL* 4.6 13.9 - - + +
958S PHE* 4.7 1.0 - - - -
961S ARG* 3.2 47.3 - - + +
964S VAL* 4.7 13.2 - - + -
965S ALA* 4.6 4.5 - - + -
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Residues in contact with TYR 631 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627S PHE* 2.8 51.5 + + + +
628S LEU* 3.6 16.2 - - + -
629S THR 3.9 0.2 - - - -
630S THR* 1.3 72.2 + - - +
632S ARG* 1.3 90.2 + - + +
633S SER 3.1 0.2 - - - -
634S PHE* 2.9 41.2 + - + -
635S CYS* 2.9 35.3 + - + -
637S PRO* 3.3 27.6 - - + +
640S LEU* 3.8 26.7 - - + -
696S TRP* 3.4 10.0 - - - -
703S ASP* 2.8 21.1 + - - -
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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