Contacts of the strand formed by residues 89 - 94 (chain 4) in PDB entry 1SVA
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 89 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514 LEU* 3.7 14.0 - - - +
524 ASN 3.3 24.6 + - - -
534 PRO* 3.8 2.8 - - - +
544 GLN* 3.7 20.0 + - - +
874 CYS 3.9 2.9 + - - -
884 TYR* 1.3 71.9 - - - +
904 VAL* 1.3 62.3 + - - +
1974 LEU* 4.4 1.0 - - - +
2004 ASP* 3.0 12.6 - - - -
2014 ASN 4.7 0.7 - - - +
2624 SER* 3.2 5.4 - - - -
2634 ALA* 3.2 36.6 + - - -
2644 VAL* 5.3 2.4 - - - -
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Residues in contact with VAL 90 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514 LEU* 4.0 4.9 - - - +
894 SER* 1.3 76.3 - - - +
914 ALA* 1.3 82.6 + - - +
1594 LEU* 6.2 1.3 - - + +
1974 LEU* 3.8 35.4 - - + +
1984 ASP* 4.7 2.5 - - - -
1994 LYS* 3.8 9.2 - - - +
2004 ASP* 2.9 47.3 + - + +
2604 TYR* 5.4 9.0 - - + -
2614 VAL 3.4 14.8 - - - +
2624 SER* 4.2 6.3 - - - +
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Residues in contact with ALA 91 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514 LEU* 3.6 24.7 - - + -
904 VAL* 1.3 89.4 - - - +
924 ARG* 1.3 62.5 + - - +
934 ILE* 4.8 5.8 - - + -
2604 TYR* 3.6 3.9 - - - +
2614 VAL* 3.0 31.7 + - + +
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Residues in contact with ARG 92 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914 ALA* 1.3 78.2 - - - +
934 ILE* 1.3 68.5 + - - +
944 PRO* 3.3 30.8 - - - +
2574 ASP 5.2 0.2 + - - -
2584 SER* 3.4 36.0 + - - -
2594 LEU 3.1 9.4 - - - +
2604 TYR* 4.1 23.8 - - + -
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Residues in contact with ILE 93 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324 ILE* 3.8 18.4 - - + -
354 LEU* 4.7 0.2 - - + -
474 VAL* 4.7 22.0 - - + -
494 CYS* 4.8 16.8 - - + -
914 ALA* 4.7 4.5 - - + +
924 ARG* 1.3 82.0 - - - +
944 PRO* 1.3 70.5 - - + +
954 LEU* 3.2 21.7 - - + +
2584 SER* 3.2 1.2 - - - -
2594 LEU* 2.5 61.2 + - + +
2614 VAL* 4.3 22.0 - - + -
2884 ILE* 5.9 0.7 - - + -
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Residues in contact with PRO 94 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324 ILE* 4.2 10.3 - - + +
354 LEU* 4.0 7.3 - - - +
924 ARG* 3.3 29.8 - - - +
934 ILE* 1.3 87.5 - - + +
954 LEU* 1.3 72.6 + - - +
964 PRO* 4.4 0.5 - - - +
2574 ASP 3.5 9.2 - - - +
2584 SER* 4.2 3.6 - - - +
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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
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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