Contacts of the strand formed by residues 107 - 119 (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 ILE 107 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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992 ASN* 3.7 20.4 - - - +
1052 GLY 3.5 13.5 - - - +
1062 ASN* 1.3 75.8 - - - +
1082 LEU* 1.3 68.0 + - - +
1092 MET* 4.8 7.2 - - + -
2942 SER* 3.7 5.8 + - - -
2952 VAL* 3.0 60.4 + - + +
2962 LYS* 4.2 0.2 - - - -
2972 ASN* 4.0 20.0 - - + +
3026 SER* 4.7 14.1 - - - +
3056 LEU* 4.0 33.4 - - + -
3066 SER* 4.8 4.0 - - - +
3096 ILE* 6.3 0.2 - - + -
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Residues in contact with LEU 108 (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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171 PRO* 3.8 25.4 - - + -
181 LYS* 5.9 1.1 - - + -
412 VAL* 4.4 14.6 - - + -
982 ILE* 3.1 31.7 - - + +
992 ASN* 2.8 22.9 + - - +
1022 LEU* 3.4 29.4 - - + +
1072 ILE* 1.3 75.4 - - - +
1092 MET* 1.3 66.8 + - - +
2572 ASP* 5.5 1.0 - - - +
2922 LYS* 4.0 25.1 - - + +
2932 ARG 3.2 27.4 - - - +
2942 SER* 3.5 10.3 - - - +
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Residues in contact with MET 109 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982 ILE* 3.5 8.8 - - - +
1072 ILE* 4.8 9.2 - - + -
1082 LEU* 1.3 79.4 - - - +
1102 TRP* 1.3 66.0 + - - +
1112 GLU 3.4 0.3 + - - -
2532 LEU* 4.6 18.8 - - + -
2542 CYS 4.3 8.7 - - - +
2552 LYS* 4.0 35.9 - - + +
2572 ASP* 5.4 6.1 - - - +
2912 ARG 3.6 0.3 - - - +
2922 LYS 3.8 0.3 - - - -
2932 ARG* 2.8 37.0 + - - +
2952 VAL* 3.2 40.8 - - + -
2962 LYS 5.3 1.8 - - - +
3056 LEU* 6.0 2.2 - - + -
3096 ILE* 5.3 10.3 - - + -
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Residues in contact with TRP 110 (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* 4.1 19.7 - - + -
392 THR* 5.4 2.5 - - - -
432 SER* 5.4 1.1 - - - -
442 PHE* 4.9 4.3 - - - -
452 THR* 4.4 10.5 - - + -
952 LEU* 3.3 46.3 - - + +
962 PRO* 2.9 39.6 + - + +
982 ILE* 3.5 21.9 - - + +
1092 MET* 1.3 72.3 - - - +
1112 GLU* 1.3 58.7 + - - +
2532 LEU* 3.5 2.0 - - - -
2542 CYS* 2.7 43.7 + - + +
2572 ASP* 4.9 11.0 + - + -
2902 LEU* 3.8 32.3 - - + -
2912 ARG 3.5 22.4 - - - -
2922 LYS* 4.2 25.4 - - + -
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Residues in contact with GLU 111 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092 MET 3.4 0.6 + - - -
1102 TRP* 1.3 75.8 - - - +
1122 ALA* 1.3 66.2 + - - +
1132 VAL* 3.5 2.6 + - - -
2452 LEU* 3.4 0.9 - - - +
2502 VAL* 2.9 5.6 - - - -
2512 GLY 2.6 34.7 + - - +
2522 PRO 3.2 7.6 - - - +
2532 LEU* 4.0 4.7 - - + -
2902 LEU* 3.2 7.4 - - - +
2912 ARG* 2.7 64.1 + - + +
2932 ARG* 2.4 55.3 + - + +
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Residues in contact with ALA 112 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1102 TRP 4.1 0.4 + - - -
1112 GLU* 1.3 71.0 - - - +
1132 VAL* 1.3 62.4 + - - +
1542 VAL* 4.4 7.0 - - + -
2442 LEU* 3.6 8.5 - - + +
2512 GLY* 3.1 9.5 - - - -
2522 PRO* 2.8 49.9 + - + +
2542 CYS* 5.0 0.2 - - - -
2592 LEU* 4.7 8.3 - - + -
2882 ILE* 4.1 11.9 - - + -
2892 THR 3.8 0.2 - - - -
2902 LEU* 3.2 19.6 - - + +
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Residues in contact with VAL 113 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112 GLU* 4.2 2.5 - - - +
1122 ALA* 1.3 76.7 - - - +
1142 THR* 1.3 77.9 + - - +
2432 VAL* 3.7 5.9 - - + +
2442 LEU* 2.7 29.2 + - - -
2452 LEU* 3.9 16.9 + - + -
2892 THR* 3.0 16.4 + - + +
2902 LEU 5.9 0.2 - - - -
2912 ARG* 3.3 52.7 - - + +
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Residues in contact with THR 114 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1132 VAL* 1.3 95.1 + - - +
1152 VAL* 1.3 68.2 + - - +
1162 LYS* 5.1 3.8 - - + -
2412 THR* 3.3 27.9 - - + +
2422 THR 3.2 8.7 + - - -
2432 VAL* 4.3 6.6 - - - +
2442 LEU* 3.7 4.0 - - - +
2872 LYS 4.6 1.3 - - - +
2882 ILE* 3.2 6.4 - - - +
2892 THR* 3.0 49.2 + - + +
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Residues in contact with VAL 115 (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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1142 THR* 1.3 78.6 - - - +
1162 LYS* 1.3 78.3 + - - +
1172 THR* 4.2 4.7 - - + +
1522 PHE* 4.5 13.9 - - + -
1542 VAL* 4.2 13.0 - - + -
2412 THR* 3.7 1.2 - - - +
2422 THR* 2.8 55.5 + - + -
2442 LEU* 3.7 27.8 - - + -
2862 PHE* 4.3 10.3 - - + -
2872 LYS 3.1 6.5 - - - +
2882 ILE* 4.1 14.8 - - + -
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Residues in contact with LYS 116 (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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1142 THR* 5.1 2.9 - - + -
1152 VAL* 1.3 77.9 - - - +
1172 THR* 1.3 63.0 + - - +
2372 THR 5.9 0.2 - - - +
2382 ASN* 3.4 28.3 + - - +
2392 THR* 4.8 3.6 - - - +
2402 ALA 3.2 25.1 - - - +
2412 THR* 3.3 26.0 + - + +
2852 TYR* 3.5 8.1 - - + +
2862 PHE* 3.3 2.9 - - - -
2872 LYS* 2.8 68.7 + - + +
2473 GLU* 3.3 23.2 + - - -
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Residues in contact with THR 117 (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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1152 VAL* 4.6 3.1 - - + +
1162 LYS* 1.3 76.7 - - - +
1182 GLU* 1.3 72.3 + - - +
1522 PHE* 3.8 36.1 - - + -
2372 THR 5.2 2.3 - - - +
2402 ALA 5.0 2.2 + - - +
2422 THR* 5.9 2.2 - - - +
2842 ARG* 2.7 29.4 + - - +
2852 TYR* 2.6 23.6 + - - -
2862 PHE* 4.4 10.1 - - - -
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Residues in contact with GLU 118 (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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1172 THR* 1.3 84.1 + - - +
1192 VAL* 1.3 70.9 + - - +
1202 ILE* 5.7 0.2 - - + -
2352 HIS 4.3 3.4 - - - +
2362 ILE* 3.0 40.7 - - + +
2372 THR 2.7 37.7 + - - +
2382 ASN* 4.4 0.5 - - - -
2842 ARG* 3.4 6.0 - - - +
2852 TYR* 2.9 39.6 + - + +
2103 PRO 4.5 0.2 - - - +
2123 PRO* 3.8 15.6 - - + +
2203 TYR* 2.6 22.2 + - - -
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Residues in contact with VAL 119 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182 GLU* 1.3 80.0 - - - +
1202 ILE* 1.3 66.7 + - - +
1212 GLY 3.5 0.3 + - - -
1222 VAL* 3.7 16.2 - - + +
1502 HIS* 4.7 7.6 - - + +
2342 LEU* 4.7 14.1 - - + -
2352 HIS 5.0 4.1 + - - +
2362 ILE* 3.3 23.4 - - - +
2652 ASP* 3.5 31.2 - - + +
2672 CYS* 5.2 2.7 - - - -
2822 LEU* 3.6 36.8 - - + -
2832 PRO 3.8 2.9 - - - +
2842 ARG* 4.1 14.6 - - + +
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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