Contacts of the strand formed by residues 89 - 94 (chain 2) 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 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512 LEU* 3.7 10.3 - - - +
522 ASN 3.3 15.2 + - - -
532 PRO* 3.7 3.1 - - - +
542 GLN* 3.6 18.4 + - - +
872 CYS 3.9 2.4 + - - -
882 TYR* 1.3 74.0 - - - +
902 VAL* 1.3 61.1 + - - +
1972 LEU* 4.4 1.8 - - - +
2002 ASP* 3.1 6.3 - - - -
2622 SER* 3.4 3.8 - - - -
2632 ALA* 3.0 40.9 + - - -
2642 VAL* 5.1 2.8 - - - -
3196 GLN* 3.3 21.8 - - - -
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Residues in contact with VAL 90 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512 LEU* 4.4 3.1 - - - -
892 SER* 1.3 75.5 - - - +
912 ALA* 1.3 76.5 + - - +
1582 PRO* 6.4 0.4 - - + -
1592 LEU* 5.9 2.2 - - + +
1972 LEU* 3.8 33.9 - - + +
1982 ASP 4.8 2.2 - - - -
1992 LYS 3.9 10.5 - - - +
2002 ASP* 2.8 38.8 + - + +
2602 TYR* 5.5 7.0 - - + -
2612 VAL 3.5 15.3 - - - +
2622 SER* 4.3 7.0 - - - +
3166 VAL* 5.5 7.2 - - + -
3176 ASP 4.4 0.4 - - - +
3186 GLY* 4.3 5.4 - - - -
3196 GLN* 3.0 23.2 + - - +
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Residues in contact with ALA 91 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512 LEU* 3.7 22.2 - - + -
902 VAL* 1.3 86.2 - - - +
922 ARG* 1.3 63.7 + - - +
932 ILE* 5.5 0.4 - - - -
2592 LEU 3.8 0.2 - - - +
2602 TYR* 3.7 3.8 - - - +
2612 VAL* 3.1 31.3 + - + +
3166 VAL* 4.8 1.8 - - - -
3186 GLY* 4.2 4.5 - - - -
3196 GLN* 3.2 26.2 - - + +
3216 MET* 4.1 12.1 - - + -
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Residues in contact with ARG 92 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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912 ALA* 1.3 77.2 - - - +
932 ILE* 1.3 64.5 + - - +
942 PRO* 3.6 26.9 - - - +
2582 SER* 3.4 36.4 + - - -
2592 LEU 3.4 4.5 - - - +
2602 TYR* 3.5 25.1 - - + -
3523 GLU* 2.7 60.5 + - - +
3533 PHE* 4.1 10.5 + - - +
3156 ARG* 5.3 0.4 - - - +
3166 VAL* 3.4 31.8 + - + +
3186 GLY* 5.3 1.0 - - - -
3196 GLN 4.2 3.6 + - - +
3216 MET* 3.7 10.9 + - - +
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Residues in contact with ILE 93 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322 ILE* 4.1 17.3 - - + -
472 VAL* 4.1 23.8 - - + -
492 CYS* 4.2 20.9 - - + -
912 ALA* 5.5 1.1 - - + +
922 ARG* 1.3 74.8 - - - +
942 PRO* 1.3 81.0 - - + +
952 LEU* 3.7 10.8 + - + +
2582 SER* 3.3 0.2 - - - -
2592 LEU* 2.6 68.0 + - + +
2612 VAL* 4.9 8.7 - - + -
2882 ILE* 5.0 0.4 - - + -
3216 MET* 3.4 25.8 - - + -
3286 VAL* 4.6 1.3 - - + -
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Residues in contact with PRO 94 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322 ILE* 4.0 11.5 - - + +
352 LEU* 4.0 3.6 - - - +
922 ARG* 3.6 22.7 - - - +
932 ILE* 1.3 94.0 - - + +
952 LEU* 1.3 71.3 + - - +
2572 ASP 3.6 6.5 - - - +
2582 SER* 4.3 4.7 - - - +
3493 TYR* 3.3 26.6 - - + -
3523 GLU 5.6 1.1 - - - +
3533 PHE* 6.1 3.1 - - + -
3216 MET* 4.6 6.1 - - + -
3226 ILE* 4.2 27.4 - - + -
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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