Contacts of the strand formed by residues 78 - 83 (chain A) in PDB entry 1GH2
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 THR 78 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL 3.4 1.7 - - - +
28A LYS* 3.5 0.9 - - - -
29A PHE* 2.7 43.7 + - - +
73A ILE* 3.9 28.4 - - + +
74A SER 5.1 0.5 + - - -
75A ALA 2.5 26.8 + - - -
76A THR* 3.8 0.6 - - - +
77A PRO* 1.3 74.0 - - - +
79A PHE* 1.3 63.2 + - - +
80A GLN* 4.1 13.5 - - - +
90A GLN* 4.5 7.6 - - - +
91A TYR 3.7 8.3 - - - +
92A GLN* 3.5 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 4.4 4.3 - - + -
27A VAL 3.2 4.7 - - - +
28A LYS* 3.3 42.6 - - + -
40A ILE* 3.8 22.2 - - + -
44A PHE* 3.5 31.0 - + - -
77A PRO* 4.0 11.9 - - + -
78A THR* 1.3 73.4 - - - +
80A GLN* 1.3 62.1 + - - +
81A PHE* 3.8 8.7 - - + -
90A GLN* 3.2 5.2 - - - +
91A TYR* 2.7 47.2 + + - +
93A GLY 3.4 24.9 - - - -
99A LEU* 3.7 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA 3.6 0.9 - - - +
26A VAL* 3.5 4.5 - - - +
27A VAL* 2.9 31.8 + - - +
29A PHE* 3.2 29.8 - - + -
71A ASN* 3.3 19.8 + - - +
73A ILE* 4.2 8.5 - - + +
78A THR* 4.1 6.1 - - - +
79A PHE* 1.3 76.3 - - - +
81A PHE* 1.3 62.2 - - - +
82A PHE* 3.3 20.1 - - + -
87A ARG* 2.7 44.7 + - + +
89A ASP 3.6 2.5 - - - +
90A GLN* 3.4 22.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.3 12.6 - - + -
25A ALA 3.3 4.0 - - - +
26A VAL* 3.9 21.1 - - + -
79A PHE* 3.8 22.4 - - + -
80A GLN* 1.3 78.0 - - - +
82A PHE* 1.3 57.6 + - - +
87A ARG* 3.3 4.5 - - - -
88A ILE* 2.7 39.0 + - + -
89A ASP* 2.9 38.1 + - + +
90A GLN 4.4 1.1 - - - -
91A TYR* 4.2 12.8 - - + -
99A LEU* 3.8 23.1 - - + -
102A LYS* 4.3 16.4 - - + -
103A ILE* 3.7 32.1 - - + -
106A HIS* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 4.0 14.6 - + - -
17A LEU* 3.7 31.2 - - + -
24A LEU* 3.4 10.5 - - - +
25A ALA* 2.7 47.7 + - + +
27A VAL* 3.7 27.1 - - + -
71A ASN* 3.6 22.4 - - - -
80A GLN* 3.3 29.6 - - + -
81A PHE* 1.3 77.0 - - - +
83A ARG* 1.3 61.1 + - - +
85A LYS* 4.1 7.2 - - - +
86A VAL 3.1 10.1 - - - +
87A ARG* 3.5 34.3 - - + -
88A ILE* 4.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER 4.0 12.6 - - - +
23A ARG 4.2 4.7 - - - -
24A LEU* 4.0 23.6 - - + +
82A PHE* 1.3 78.4 - - - +
84A ASN* 1.3 74.6 + - - +
86A VAL* 3.1 22.7 + - - +
88A ILE* 3.6 34.2 - - + +
105A GLN 5.0 0.2 + - - -
106A HIS* 3.0 46.9 + - - +
108A GLU* 2.7 29.3 + - - -
----------------------------------------------------------
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