Contacts of the strand formed by residues 284 - 295 (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 ARG 284 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502 PHE* 3.3 4.2 - - - +
512 LEU* 3.0 31.4 + - + +
1172 THR* 2.7 29.1 + - - +
1182 GLU* 3.4 10.8 - - - +
1192 VAL* 4.1 14.0 - - + +
1202 ILE* 3.9 4.7 - - - -
1502 HIS* 5.1 5.7 - - - +
1512 PHE 3.8 14.3 + - - +
1522 PHE* 3.9 21.0 - - - +
2632 ALA* 3.6 12.1 - - + -
2642 VAL 4.1 0.2 + - - -
2652 ASP* 2.5 54.9 + - - +
2822 LEU 3.6 0.2 + - - -
2832 PRO* 1.3 74.3 - - - +
2852 TYR* 1.3 62.1 + - - +
2862 PHE* 3.3 32.7 - - + -
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Residues in contact with TYR 285 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482 GLU* 2.7 30.2 + - + -
492 CYS 4.4 5.8 - - - -
502 PHE* 4.1 5.2 - - + -
1162 LYS* 3.5 14.9 - - + +
1172 THR* 2.6 37.9 + - - -
1182 GLU* 2.9 18.6 + - + +
1202 ILE* 3.8 16.5 - - + +
2842 ARG* 1.3 71.4 - - - +
2862 PHE* 1.3 72.4 + - - +
2872 LYS* 3.4 35.7 - - + +
2123 PRO* 3.3 35.9 + - + -
2133 SER* 3.3 31.2 - - - -
3296 GLU* 5.3 3.8 - - + -
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Residues in contact with PHE 286 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472 VAL 4.3 0.9 - - - -
482 GLU* 3.3 5.2 - - - -
492 CYS* 3.2 51.4 + - - +
502 PHE* 4.4 1.3 - - - -
512 LEU* 4.1 9.9 - - + -
1152 VAL* 4.3 9.4 - - + -
1162 LYS 3.3 4.9 - - - -
1172 THR* 4.4 2.0 - - - -
1522 PHE* 3.6 25.1 - + + -
1542 VAL* 4.0 16.4 - - + -
2612 VAL* 3.7 31.9 - - + -
2622 SER 3.9 3.6 - - - -
2632 ALA* 3.8 12.1 - - + -
2842 ARG* 3.3 40.8 - - + -
2852 TYR* 1.3 85.6 - - - +
2872 LYS* 1.3 64.0 + - - +
2882 ILE* 3.9 8.1 - - + -
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Residues in contact with LYS 287 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462 GLU* 3.5 40.1 + - + -
472 VAL 3.3 6.1 - - - +
482 GLU* 3.8 16.1 + - + -
1142 THR* 3.3 2.3 - - - +
1152 VAL* 3.1 5.4 - - - +
1162 LYS* 2.8 64.5 + - + +
2852 TYR* 3.4 30.7 + - + +
2862 PHE* 1.3 75.3 - - - +
2882 ILE* 1.3 65.4 + - - +
2892 THR* 4.2 5.9 + - - +
2163 GLU* 4.7 16.4 + - - +
2473 GLU* 5.8 2.6 + - - -
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Residues in contact with ILE 288 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452 THR 3.8 0.5 - - - +
462 GLU* 3.5 2.6 - - - -
472 VAL* 2.9 41.0 + - + +
492 CYS* 4.6 4.9 - - - -
932 ILE* 5.0 2.5 - - + -
1122 ALA* 4.1 11.7 - - + -
1142 THR 3.2 7.4 - - - +
1152 VAL* 4.1 14.6 - - + -
1542 VAL* 4.4 11.7 - - + -
2442 LEU* 5.0 0.2 - - + -
2592 LEU* 3.9 21.3 - - + -
2612 VAL* 3.9 27.4 - - + -
2862 PHE* 3.9 15.3 - - + -
2872 LYS* 1.3 75.4 - - - +
2892 THR* 1.3 67.6 + - - +
2902 LEU* 3.6 29.0 + - + -
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Residues in contact with THR 289 (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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442 PHE* 4.3 16.4 - - + -
452 THR 3.4 11.0 - - - +
462 GLU* 4.0 20.1 - - + +
1132 VAL* 3.0 33.7 + - + +
1142 THR* 3.0 36.9 + - + +
2872 LYS* 4.2 6.1 + - - +
2882 ILE* 1.3 75.7 - - - +
2902 LEU* 1.3 62.7 + - - +
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Residues in contact with LEU 290 (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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352 LEU* 5.7 1.1 - - + -
442 PHE* 2.8 25.6 - - - +
452 THR* 2.8 22.7 + - - +
472 VAL* 4.2 19.3 - - + -
952 LEU* 4.1 23.3 - - + -
1102 TRP* 3.8 20.4 - - + -
1112 GLU* 3.2 7.4 - - - +
1122 ALA* 3.2 38.1 - - + -
1132 VAL* 5.7 0.2 - - - -
2542 CYS* 5.1 0.9 - - - -
2592 LEU* 3.9 25.8 - - + -
2882 ILE* 3.6 10.8 - - + +
2892 THR* 1.3 78.5 - - - +
2912 ARG* 1.3 61.4 + - - +
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Residues in contact with ARG 291 (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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432 SER 4.4 2.5 - - - +
442 PHE* 4.1 12.1 - - + -
1102 TRP* 3.5 10.1 - - - -
1112 GLU* 2.7 77.8 + - + +
1132 VAL* 3.3 20.6 - - + +
2452 LEU* 3.9 16.3 - - - +
2492 GLY 3.3 17.0 + - - -
2902 LEU* 1.3 75.8 - - - +
2922 LYS* 1.3 71.0 + - - +
2932 ARG* 3.4 7.2 - - - +
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Residues in contact with LYS 292 (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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181 LYS* 4.8 11.1 - - - +
392 THR* 3.0 36.5 + - - +
402 GLY 2.6 31.9 + - - +
412 VAL* 3.4 23.8 + - - +
432 SER* 3.8 14.6 + - - +
982 ILE* 4.2 24.1 - - + +
1082 LEU* 4.0 22.3 - - + +
1092 MET 3.9 3.1 - - - -
1102 TRP* 4.2 23.1 - - + -
2912 ARG* 1.3 80.7 - - - +
2932 ARG* 1.3 61.3 + - - +
2942 SER 4.0 1.4 + - - -
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Residues in contact with ARG 293 (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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211 VAL* 3.4 35.1 - - - +
1082 LEU* 3.2 5.9 - - - -
1092 MET* 2.8 44.8 + - - +
1112 GLU* 2.4 65.6 + - + +
2482 GLN 4.4 2.6 + - - -
2492 GLY 2.9 20.2 + - - -
2502 VAL* 3.5 16.7 - - - +
2532 LEU* 4.2 15.9 - - + -
2912 ARG* 3.4 11.1 + - - +
2922 LYS* 1.3 72.9 - - - +
2942 SER* 1.3 80.2 + - - +
2952 VAL* 3.7 7.1 + - + +
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Residues in contact with SER 294 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171 PRO* 4.3 8.3 - - - +
181 LYS* 2.7 39.5 + - - +
191 GLU 4.4 1.6 - - - -
201 PRO* 3.6 28.1 - - - +
211 VAL* 4.8 0.5 + - - +
1062 ASN* 4.6 2.8 + - - -
1072 ILE 3.7 7.5 + - - -
1082 LEU* 3.5 16.0 - - - +
2922 LYS 4.0 1.0 + - - -
2932 ARG* 1.3 88.6 + - - +
2952 VAL* 1.3 64.7 + - - +
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Residues in contact with VAL 295 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201 PRO* 3.4 17.6 - - - +
1052 GLY 4.9 0.7 - - - +
1062 ASN* 5.3 0.7 - - - -
1072 ILE* 3.0 44.3 + - + +
1092 MET* 3.2 45.1 - - + -
2532 LEU* 4.2 14.1 - - + -
2932 ARG* 4.0 20.6 - - + +
2942 SER* 1.3 80.0 + - - +
2962 LYS* 1.3 68.9 - - - +
3056 LEU* 6.4 0.2 - - + -
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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