Contacts of the strand formed by residues 249 - 261 (chain 2) in PDB entry 1G6Q
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 ASP 249 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1742 GLU* 3.9 21.3 - - - +
2132 ASN 5.2 0.3 - - - +
2162 ASN* 3.5 19.5 - - + +
2472 ARG* 3.2 38.9 + - - +
2482 GLN* 1.3 77.0 - - - +
2502 MET* 1.3 65.1 + - - +
2512 ILE* 5.3 0.4 - - - -
2962 ASP* 4.4 1.7 - - - +
2972 ALA* 2.9 33.3 + - - +
2484 GLN* 4.2 4.5 + - - -
2136 ASN* 3.8 17.5 + - - +
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Residues in contact with MET 250 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1742 GLU* 3.5 18.8 - - + +
1762 SER* 3.9 22.4 - - - +
2162 ASN* 3.1 12.8 - - - +
2492 ASP* 1.3 79.4 + - - +
2512 ILE* 1.3 58.4 + - - +
2522 ASN* 3.8 8.0 - - - +
2942 ASP* 3.5 38.6 - - + +
2952 LEU 3.3 8.5 - - - +
2962 ASP* 3.8 23.1 - - + +
2126 ARG* 3.3 54.7 - - + +
2136 ASN* 5.5 2.4 + - - +
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Residues in contact with ILE 251 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1722 GLY* 4.0 11.0 - - - -
1732 LEU 3.6 3.1 - - - +
2162 ASN* 3.5 18.6 - - - +
2172 THR* 3.8 20.9 - - + -
2452 ALA* 4.8 5.8 - - + -
2492 ASP 5.0 0.4 - - - +
2502 MET* 1.3 71.1 - - - +
2522 ASN* 1.3 62.1 + - - +
2532 GLY 3.5 20.9 - - - +
2912 PHE* 3.9 14.7 - - + -
2932 ASP 4.0 0.9 - - - +
2942 ASP* 3.8 1.4 - - - -
2952 LEU* 3.0 41.1 + - + +
2972 ALA* 3.8 26.9 - - + -
3032 ILE* 4.0 22.4 - - + -
3272 PHE* 4.8 5.2 - - + -
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Residues in contact with ASN 252 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1732 LEU* 2.8 10.3 + - - +
1742 GLU* 3.7 2.4 - - - +
1752 ASP* 2.8 18.5 + - + +
1762 SER* 2.6 44.7 + - - +
1792 LYS* 2.8 39.2 + - + +
1802 ASP* 5.6 0.8 + - - -
2502 MET* 4.1 9.3 - - - +
2512 ILE* 1.3 76.3 - - - +
2532 GLY* 1.3 58.5 + - - +
2902 TYR* 3.6 6.9 - - + -
2912 PHE* 3.0 12.2 + - - -
2942 ASP* 2.8 37.1 + - - +
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Residues in contact with GLY 253 (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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1722 GLY* 3.5 5.9 - - - -
1732 LEU* 2.9 26.2 + - - +
2512 ILE* 3.4 8.4 - - - +
2522 ASN* 1.3 80.0 - - - +
2542 ILE* 1.3 64.0 + - - +
2892 PHE 3.2 12.6 - - - -
2902 TYR* 4.2 3.1 - - - -
2912 PHE* 3.4 18.0 - - - -
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Residues in contact with ILE 254 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1702 LEU* 3.8 23.1 - - + -
1712 ALA 3.2 12.6 - - - +
1732 LEU* 4.3 3.8 - - - +
2412 PHE* 5.2 4.0 - - + -
2432 LEU* 4.4 17.3 - - + -
2532 GLY* 1.3 77.0 - - - +
2552 VAL* 1.3 59.3 + - - +
2562 THR* 3.6 27.1 - - + -
2872 THR 4.0 0.3 - - - +
2882 ILE* 3.5 4.5 - - - +
2892 PHE* 2.8 44.4 + - + +
2912 PHE* 3.3 26.9 - - + -
3072 LEU* 4.1 4.3 - - + -
3232 ILE* 3.8 25.6 - - + -
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Residues in contact with VAL 255 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1702 LEU* 3.2 2.1 - - - -
1712 ALA* 2.8 50.6 + - + +
1722 GLY 4.4 7.2 - - - +
1732 LEU* 4.3 12.7 - - + +
2102 VAL* 3.9 19.3 - - + -
2152 VAL* 4.6 7.6 - - + -
2542 ILE* 1.3 74.2 - - - +
2562 THR* 1.3 63.4 + - - +
2572 TRP* 3.2 12.0 - - + -
2772 PRO* 4.2 13.5 - - + -
2862 GLN* 3.5 33.4 - - + -
2872 THR 3.8 4.3 - - - +
2882 ILE* 4.5 3.6 - - + +
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Residues in contact with THR 256 (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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1372 PHE* 3.4 38.0 - - + -
1692 HIS 3.2 14.8 - - - +
1702 LEU* 3.8 4.7 - - + -
2222 LEU* 5.4 1.6 - - + -
2542 ILE* 3.6 30.3 - - + -
2552 VAL* 1.3 75.1 - - - +
2572 TRP* 1.3 69.2 + - - +
2862 GLN* 3.3 6.1 - - - +
2872 THR* 2.9 39.4 + - - -
2892 PHE* 3.6 7.1 - - + -
3072 LEU* 4.8 2.9 - - + -
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Residues in contact with TRP 257 (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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1362 TYR 5.9 1.6 - - - -
1372 PHE* 5.9 2.7 - - - +
1682 ILE* 3.4 8.3 - - - +
1692 HIS* 2.8 51.0 + + + +
1702 LEU* 3.7 20.4 - - - -
1712 ALA* 3.8 6.7 - - + -
2192 SER* 3.9 20.6 - - - -
2552 VAL* 3.2 25.6 - - + -
2562 THR* 1.3 86.0 - - - +
2582 PHE* 1.3 79.8 + - - +
2592 ASP* 3.7 20.8 + - - -
2742 SER* 3.8 2.4 + - - -
2752 THR* 3.5 13.7 - - - +
2762 GLY* 3.3 33.1 - - - -
2772 PRO* 3.6 22.9 - - + -
2782 HIS* 5.1 11.7 - + - -
2852 LYS 4.9 0.7 - - - +
2862 GLN* 4.2 3.6 - - + +
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Residues in contact with PHE 258 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1342 MET* 4.0 17.5 - - + -
1352 GLY 3.4 19.7 - - - -
1362 TYR 3.8 10.3 - - - -
1372 PHE* 4.3 1.1 - - - -
1382 LEU* 3.5 40.2 - - + -
1672 SER 3.0 16.2 - - - +
1682 ILE* 4.4 1.3 - - + -
1692 HIS* 4.7 0.7 - - - +
2572 TRP* 1.3 81.2 - - - +
2592 ASP* 1.3 66.6 + - - +
2602 ILE* 3.9 20.4 - - + -
2732 PHE 4.3 0.2 - - - +
2742 SER 3.7 0.2 - - - -
2752 THR* 2.8 59.6 + - + +
2842 TRP* 3.5 40.4 - + + -
2852 LYS 6.1 0.2 - - - -
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Residues in contact with ASP 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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1662 CYS* 3.2 5.7 - - - +
1672 SER* 2.9 39.8 + - - +
1692 HIS* 3.5 22.2 + - - -
2572 TRP* 3.7 8.0 + - - -
2582 PHE* 1.3 77.0 - - - +
2602 ILE* 1.3 71.0 + - - +
2612 VAL* 5.6 2.7 - - + -
2732 PHE 3.5 5.6 - - - +
2742 SER* 2.7 33.4 + - - -
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Residues in contact with ILE 260 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1332 TRP* 5.0 0.7 - - + -
1342 MET* 4.1 18.8 - - + -
1382 LEU* 4.3 0.2 - - + -
1632 PRO* 3.6 30.3 - - + -
1652 LYS 3.6 1.1 - - - +
1662 CYS* 3.5 20.0 - - + -
2582 PHE* 3.9 23.8 - - + -
2592 ASP* 1.3 88.2 - - - +
2612 VAL* 1.3 67.8 + - - +
2622 PHE* 3.8 6.5 - - + -
2722 GLU* 3.2 7.1 - - - +
2732 PHE* 2.8 71.1 + - + +
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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
----------------------------------------------------------
1632 PRO* 3.1 16.5 - - - +
1642 ASP 3.1 10.4 + - - -
1652 LYS* 2.8 51.0 + - + +
1662 CYS* 5.9 0.2 - - - -
2592 ASP* 5.6 2.7 - - + -
2602 ILE* 1.3 78.9 - - - +
2622 PHE* 1.3 79.2 + - - +
2702 PRO* 4.2 19.5 - - + -
2712 VAL 3.9 4.9 - - - +
2722 GLU* 4.3 18.2 - - + +
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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