Contacts of the strand formed by residues 258 - 266 (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 258 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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922 ARG* 3.4 42.2 + - - -
932 ILE 3.3 6.5 - - - -
942 PRO* 4.5 0.9 - - - +
952 LEU* 4.3 2.6 - - - +
1562 GLY* 4.2 0.7 - - - +
2542 CYS* 3.1 25.6 - - - +
2562 ALA* 2.3 30.7 + - - +
2572 ASP* 1.3 74.5 + - - +
2592 LEU* 1.3 60.8 + - - +
2602 TYR* 3.9 20.4 + - - -
3523 GLU* 4.6 6.6 - - - +
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Residues in contact with LEU 259 (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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472 VAL* 5.4 2.5 - - + -
912 ALA 3.8 0.7 - - - +
922 ARG* 3.4 3.7 - - - -
932 ILE* 2.6 63.0 + - + +
952 LEU* 4.2 8.5 - - + -
1122 ALA* 4.7 13.7 - - + -
1542 VAL* 5.0 4.9 - - + -
1552 GLY 3.7 11.2 - - - +
2542 CYS* 3.6 23.6 - - - -
2582 SER* 1.3 72.0 - - - +
2602 TYR* 1.3 69.7 + - - +
2612 VAL* 3.9 2.0 + - + -
2882 ILE* 3.9 33.4 - - + -
2902 LEU* 3.9 22.7 - - + -
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Residues in contact with TYR 260 (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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902 VAL* 5.5 6.3 - - + -
912 ALA 3.7 4.0 - - - +
922 ARG* 3.5 38.4 - - + -
1532 ALA 3.7 0.9 - - - +
1542 VAL* 3.4 6.1 - - - +
1552 GLY 2.8 43.0 + - - +
1562 GLY 3.7 4.5 - - - -
1572 GLU* 3.3 42.6 - - - +
1582 PRO* 3.6 30.1 - - + +
1592 LEU 5.2 1.1 - - - +
2562 ALA* 4.7 6.1 - - + +
2582 SER* 3.9 21.0 - - - -
2592 LEU* 1.3 73.9 - - - +
2612 VAL* 1.3 64.3 + - - +
2622 SER* 4.2 5.0 + - - +
3523 GLU* 4.0 9.0 + - - -
3136 THR* 4.0 17.7 - - + +
3146 GLN 4.2 0.9 + - - -
3166 VAL* 3.8 15.9 - - + -
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Residues in contact with VAL 261 (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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492 CYS* 4.5 10.3 - - - -
512 LEU* 3.6 28.7 - - + -
902 VAL* 3.5 2.6 - - - +
912 ALA* 3.1 33.4 + - + +
932 ILE* 4.9 8.5 - - + -
1532 ALA 3.5 1.6 - - - -
1542 VAL* 4.1 7.4 - - + -
2592 LEU* 3.9 3.3 + - + +
2602 TYR* 1.3 78.0 - - - +
2622 SER* 1.3 66.4 + - - +
2862 PHE* 3.7 31.6 - - + -
2882 ILE* 3.9 28.3 - - + -
3216 MET* 6.5 0.2 - - - -
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Residues in contact with SER 262 (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* 4.1 1.6 - - - -
892 SER 3.4 11.7 - - - -
902 VAL* 4.3 11.1 - - - +
1512 PHE* 4.6 2.5 - - - -
1522 PHE* 3.1 3.8 - - - +
1532 ALA* 2.7 42.9 + - - +
1592 LEU* 4.3 30.1 + - - +
1972 LEU* 4.4 4.5 - - - -
2602 TYR* 4.2 5.0 + - - +
2612 VAL* 1.3 82.6 + - - +
2632 ALA* 1.3 65.5 + - - +
2862 PHE* 3.9 2.0 - - - -
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Residues in contact with ALA 263 (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* 3.8 11.4 - - + +
882 TYR* 5.6 0.6 - - - -
892 SER* 3.0 31.3 + - - +
1512 PHE* 3.2 10.4 - - - +
1522 PHE* 3.7 1.8 - - + +
2622 SER* 1.3 78.0 - - - +
2642 VAL* 1.3 72.3 + - - +
2652 ASP* 4.5 2.9 - - - +
2842 ARG* 3.6 33.7 - - + +
2862 PHE* 3.8 6.1 - - + -
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Residues in contact with VAL 264 (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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532 PRO* 6.5 0.2 - - - -
552 MET* 6.1 1.6 - - - -
862 PRO* 6.2 0.7 - - + -
872 CYS 4.9 5.2 - - - +
882 TYR* 3.2 39.9 - - + -
892 SER* 5.1 3.4 - - - -
1492 PHE* 3.9 11.4 - - + -
1502 HIS* 3.1 2.9 - - - -
1512 PHE* 2.7 45.1 + - + +
2052 VAL* 3.5 16.6 - - + -
2632 ALA* 1.3 84.3 - - - +
2652 ASP* 1.3 70.5 + - - +
2662 ILE* 3.4 27.1 - - + -
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Residues in contact with ASP 265 (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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532 PRO* 5.6 5.8 - - + +
552 MET* 4.4 4.1 - - - -
1192 VAL* 3.5 14.9 - - + +
1492 PHE 3.3 4.0 - - - -
1502 HIS* 3.1 25.1 + - + +
2632 ALA* 4.5 1.0 - - - +
2642 VAL* 1.3 83.4 + - - +
2662 ILE* 1.3 62.3 + - - +
2672 CYS* 3.0 9.9 + - - -
2812 GLY* 3.2 19.1 - - - -
2822 LEU 3.6 24.4 + - - +
2842 ARG* 2.5 42.9 + - - +
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Residues in contact with ILE 266 (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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1261 LEU* 4.6 9.2 - - + -
552 MET* 3.3 28.5 - - + -
862 PRO* 4.7 9.4 - - + -
1472 SER 4.1 3.1 - - - +
1482 ASN* 3.1 7.2 - - - +
1492 PHE* 2.7 51.6 + - + +
1502 HIS* 3.5 2.3 + - - -
2052 VAL* 4.5 13.5 - - + -
2642 VAL* 3.4 28.3 - - + -
2652 ASP* 1.3 70.5 - - - +
2672 CYS* 1.3 58.5 + - - +
2682 GLY* 3.6 10.5 - - - +
2792 TRP* 3.3 38.4 - - + -
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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