Contacts of the strand formed by residues 61 - 69 (chain D) in PDB entry 3G4C
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 VAL 61 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C MET* 3.7 10.4 - - + +
61C VAL* 4.2 15.3 - - + -
161C THR* 4.3 2.9 - - + -
16D VAL* 3.2 5.2 - - - +
17D MET* 2.7 64.7 + - + -
58D GLU 3.9 13.5 - - - +
60D ILE* 1.3 82.2 - - - +
62D PHE* 1.3 65.8 + - - +
161D THR* 3.6 28.5 - - + -
162D VAL 3.5 11.9 - - - +
163D ASN* 4.1 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C MET* 4.4 0.7 - - - -
13D LEU* 3.9 10.3 - - + -
15D ASP 3.5 5.2 - - - +
16D VAL* 3.7 20.0 - - + -
60D ILE* 3.7 18.8 - - + -
61D VAL* 1.3 76.8 - - - +
63D THR* 1.3 62.3 + - - +
64D PHE* 3.5 27.1 - + + -
160D TRP 4.3 0.2 - - - -
161D THR* 3.2 8.8 - - - +
162D VAL 2.9 36.1 + - - +
164D ALA* 4.6 6.7 - - - -
167D LEU* 3.9 15.7 - - + -
193D ILE* 4.5 1.1 - - + -
194D PHE* 3.4 43.5 - + - -
197D LYS* 3.8 24.0 - - + -
198D CYS* 3.9 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C MET* 3.4 19.8 - - - +
59C HIS* 4.2 9.5 + - + +
13D LEU* 3.9 3.1 - - - +
14D VAL* 2.8 44.2 + - + -
15D ASP* 2.9 20.2 + - - +
62D PHE* 1.3 72.8 - - - +
64D PHE* 1.3 59.0 - - - +
159D PHE* 3.9 28.0 - - + -
160D TRP 3.2 5.6 - - - +
161D THR* 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D VAL* 3.9 10.1 - - + -
12D GLU 3.3 11.0 - - - +
13D LEU* 3.9 6.7 - - + -
14D VAL* 3.9 3.4 - - - -
62D PHE* 3.5 36.1 - + + -
63D THR* 1.3 74.8 - - - +
65D HIS* 1.3 61.2 + - - +
66D VAL* 3.9 18.2 - - + -
158D PHE 3.8 0.3 - - - +
159D PHE* 3.3 7.6 - - - +
160D TRP* 2.8 64.2 + + + +
162D VAL* 3.9 13.0 - - + -
167D LEU* 4.4 7.0 - - + -
190D ILE* 3.9 29.2 - - + -
193D ILE* 3.6 36.1 - - + -
194D PHE 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 4.0 8.3 + - + +
30C SER* 5.1 0.2 - - - -
31C PHE* 4.1 12.9 - - - +
10D PHE* 3.8 19.2 - + - -
11D VAL* 3.5 1.9 - - - -
12D GLU* 2.7 68.7 + - + +
14D VAL* 3.7 15.1 - - + +
64D PHE* 1.3 72.7 - - - +
66D VAL* 1.3 68.1 + - - +
157D ARG* 3.3 39.3 + - - +
158D PHE 3.5 11.0 - - - -
159D PHE* 3.7 17.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D PHE* 3.4 13.0 - - - +
11D VAL* 4.2 7.6 - - + -
64D PHE* 3.9 20.9 - - + +
65D HIS* 1.3 80.0 - - - +
67D LYS* 1.3 60.1 + - - +
68D ALA* 4.0 3.4 - - + -
76D TRP* 3.7 31.4 - - + -
157D ARG* 3.2 6.8 - - - +
158D PHE* 2.9 71.4 + - + +
160D TRP* 4.9 1.1 - - + -
186D TYR* 3.9 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LYS* 3.1 26.1 + - - +
9D GLY* 3.3 1.7 - - - -
10D PHE* 3.0 54.5 + - + +
66D VAL* 1.3 71.3 - - - +
68D ALA* 1.3 55.3 + - - +
97D GLU* 2.9 39.1 + - - -
155D TYR* 3.8 22.0 - - + -
156D THR 3.3 10.8 - - - +
157D ARG* 3.7 14.4 - - + +
186D TYR* 2.6 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D VAL* 4.0 11.2 + - + -
67D LYS* 1.3 76.4 - - - +
69D PRO* 1.3 74.7 - - + +
72D VAL* 4.1 13.0 - - + -
73D ALA* 4.7 1.8 - - + +
76D TRP* 5.1 0.2 - - + -
155D TYR* 3.4 6.1 - - - -
156D THR* 2.7 36.9 + - - +
158D PHE* 4.3 11.7 - - + -
186D TYR* 3.2 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 3.8 12.8 - - + -
68D ALA* 1.3 91.1 - - + +
70D ILE* 1.3 66.7 + - - +
71D PHE* 3.5 29.4 - - + -
72D VAL* 3.0 17.6 + - + +
73D ALA* 3.0 18.2 + - - +
99D TYR* 3.8 20.6 - - + -
153D ASN 3.8 13.0 - - - +
154D LEU 3.4 8.1 - - - +
155D TYR* 3.6 10.0 - - + -
186D TYR* 3.7 9.6 - - - +
----------------------------------------------------------
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