Contacts of the strand formed by residues 237 - 244 (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 PHE 237 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1372 PHE* 4.5 5.2 - + - -
1392 LEU* 3.9 16.8 - - + -
1682 ILE* 3.9 22.4 - - + -
2222 LEU* 4.4 9.4 - - + -
2232 ILE* 3.9 28.7 - - + -
2252 PHE* 4.0 8.5 - + - -
2342 ASP 4.2 9.6 - - - +
2352 LEU 3.2 15.7 - - - -
2362 ALA* 1.3 76.1 - - - +
2382 LYS* 1.3 65.1 + - - +
2392 SER* 3.8 16.8 - - - -
3072 LEU* 4.2 19.1 - - + -
3082 VAL* 3.4 2.6 - - - +
3092 CYS* 2.7 65.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 238 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2232 ILE* 5.5 1.6 - - - +
2372 PHE* 1.3 78.4 - - - +
2392 SER* 1.3 68.0 + - - +
2402 ASN* 6.1 0.4 - - - +
3062 GLU* 4.2 21.1 - - + +
3072 LEU 3.5 4.9 - - - -
3082 VAL* 3.9 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 239 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2222 LEU* 2.9 49.2 + - - -
2232 ILE* 4.0 6.9 - - - +
2372 PHE* 3.8 12.1 - - - -
2382 LYS* 1.3 77.8 + - - +
2402 ASN* 1.3 65.4 + - - +
2412 PHE* 4.7 0.2 - - - -
3062 GLU* 3.1 8.0 - - - +
3072 LEU 2.8 35.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 240 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2202 ASP* 3.9 4.3 - - - +
2212 LYS 4.6 5.5 - - - +
2222 LEU* 4.5 2.8 - - - +
2392 SER* 1.3 82.7 - - - +
2412 PHE* 1.3 63.0 + - - +
3052 GLY 3.4 12.9 + - - -
3062 GLU* 4.2 15.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 241 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1702 LEU* 3.8 40.8 - - + -
2202 ASP* 3.2 13.0 - - - +
2222 LEU* 4.0 18.4 - - + -
2402 ASN* 1.3 78.2 - - - +
2422 LYS* 1.3 63.1 + - - +
2432 LEU* 3.9 15.0 - - + -
2542 ILE* 5.2 6.1 - - + -
2912 PHE* 5.7 0.9 - + - -
3032 ILE* 3.9 25.8 - - + -
3042 GLU* 3.3 3.8 - - - +
3052 GLY* 2.9 49.5 + - - -
3062 GLU* 3.3 31.6 - - - -
3072 LEU* 4.1 4.0 - - + -
3232 ILE* 4.6 13.5 - - + -
3242 SER 4.2 5.4 - - - -
3252 TYR* 4.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2182 THR* 4.6 2.9 + - - -
2192 SER 5.2 0.7 - - - +
2202 ASP* 3.1 25.2 + - - +
2412 PHE* 1.3 76.3 - - - +
2432 LEU* 1.3 65.6 + - - +
2442 THR* 4.3 11.6 + - - +
3022 THR* 3.3 23.7 + - - +
3032 ILE 3.2 3.8 - - - +
3042 GLU* 3.5 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1702 LEU* 3.4 31.2 - - + +
1712 ALA* 3.7 4.7 - - - +
1722 GLY* 3.3 30.5 - - - +
2172 THR* 3.5 16.3 - - + +
2182 THR* 3.4 19.5 - - - +
2202 ASP 3.9 4.3 - - - +
2412 PHE* 3.9 20.4 - - + -
2422 LYS* 1.3 80.5 - - - +
2442 THR* 1.3 63.2 + - - +
2452 ALA 4.0 0.3 + - - -
2542 ILE* 4.4 9.6 - - + -
3022 THR* 3.5 4.2 + - - -
3032 ILE* 2.7 48.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 244 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2172 THR* 3.9 2.5 - - - -
2182 THR* 2.7 52.4 + - - +
2422 LYS* 4.3 12.0 - - - +
2432 LEU* 1.3 74.0 + - - +
2452 ALA* 1.3 64.3 + - - +
2462 LYS 3.3 0.7 + - - -
3002 GLY* 3.8 19.5 - - - +
3012 ASP 3.7 2.7 - - - -
3022 THR* 3.9 9.4 + - - +
3324 ILE* 3.7 30.2 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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