Contacts of the strand formed by residues 67 - 73 (chain B) in PDB entry 3GGS
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 ARG 67 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B THR* 3.4 14.6 + - - -
47B ILE* 3.8 27.7 - - - +
48B PHE 3.4 13.7 - - - +
49B ASP* 3.8 16.3 + - - +
50B TYR* 3.3 20.2 + - - +
64B HIS* 6.4 0.2 - - + -
66B GLY* 1.3 76.7 - - - +
68B LEU* 1.3 60.8 + - - +
69B VAL* 3.9 12.7 - - + +
81B MET 4.0 0.3 - - - -
82B GLN* 3.0 64.3 + - + +
296B SO4 3.2 42.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 4.0 22.2 - - + -
46B GLN 3.9 0.3 - - - +
47B ILE* 3.6 1.0 - - - +
48B PHE* 2.8 41.7 + - + +
50B TYR* 3.8 7.8 - - + -
53B ILE* 3.7 24.5 - - + -
56B PHE* 4.0 13.0 - - + -
67B ARG* 1.3 73.3 - - - +
69B VAL* 1.3 63.5 + - - +
70B PHE* 4.2 6.5 - - + -
79B VAL* 3.8 17.3 - - + -
80B MET 3.4 11.4 - - - +
81B MET* 3.9 17.0 - - + -
103B PHE* 3.9 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B THR* 3.9 25.1 - - + +
42B LEU* 3.4 25.7 - - + +
45B ALA* 3.9 12.3 - - + -
46B GLN 3.4 8.3 - - - +
47B ILE* 4.1 15.5 - - + -
67B ARG* 3.9 28.0 - - + +
68B LEU* 1.3 79.0 - - - +
70B PHE* 1.3 68.6 + - - +
78B CYS 4.0 0.2 - - - +
79B VAL* 3.6 1.2 - - - -
80B MET* 2.8 40.7 + - - +
82B GLN* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 4.3 17.0 - - + -
18B LEU* 6.0 0.9 - - + -
21B THR* 4.3 15.9 - - + +
23B HIS* 3.9 35.0 - - + -
25B PRO* 3.9 20.9 - - + -
42B LEU* 4.3 0.9 - - - -
45B ALA* 3.1 9.0 - - - +
46B GLN* 2.9 33.1 + - + +
48B PHE* 3.5 40.8 - + - -
68B LEU* 4.6 6.1 - - + -
69B VAL* 1.3 76.2 - - - +
71B GLY* 1.3 58.0 + - - +
78B CYS 3.3 8.3 - - - -
79B VAL* 3.5 35.0 - - + +
106B LEU* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B HIS* 3.7 18.5 + - - -
42B LEU* 3.9 10.5 - - - +
43B THR 3.5 10.5 - - - -
45B ALA* 4.1 1.3 - - - -
69B VAL 4.0 0.2 + - - -
70B PHE* 1.3 75.9 - - - +
72B PHE* 1.3 61.2 + - - -
76B ARG 3.3 0.3 - - - +
77B ALA* 3.6 1.0 - - - -
78B CYS* 2.7 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B HIS* 3.8 25.1 - + - -
41B LYS 4.1 1.0 - - - +
42B LEU* 3.3 4.4 - - - -
43B THR* 2.7 54.6 + - - +
44B GLN* 3.9 32.1 - - + -
71B GLY* 1.3 72.3 - - - -
73B LEU* 1.3 60.0 + - - +
74B ASN 4.1 1.2 + - - -
75B GLY* 3.4 31.4 - - - +
76B ARG 3.1 3.8 - - - -
77B ALA* 3.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 3.9 24.0 - - + -
38B LEU* 4.4 12.3 - - + +
41B LYS* 3.8 32.5 - - + +
42B LEU* 3.7 15.1 - - + +
72B PHE* 1.3 71.6 - - - +
74B ASN* 1.3 75.6 + - - +
75B GLY 3.1 0.2 - - - -
76B ARG* 2.9 23.8 + - - +
78B CYS* 4.1 9.9 - - - -
80B MET* 4.1 5.4 - - + -
275B VAL* 4.4 1.6 - - + +
276B SER* 3.2 36.1 - - - +
279B MET* 3.6 23.8 - - + +
----------------------------------------------------------
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