Contacts of the helix formed by residues 86 - 96 (chain A) in PDB entry 1GPM
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 CYS 86 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLY* 4.3 1.3 - - - -
85A VAL* 1.3 68.1 - - - +
87A TYR* 1.3 60.6 + - - +
89A MET* 2.9 20.6 + - - +
90A GLN* 3.0 19.9 + - - +
142A SER* 3.4 25.1 - - - +
178A VAL 2.7 19.2 + - - -
179A GLN* 4.3 6.5 - - - +
180A PHE 3.7 20.0 - - - -
181A HIS* 3.1 39.7 - - - +
529A CIT 3.2 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.6 39.3 - + + -
58A GLY 3.7 0.4 - - - -
59A GLY* 3.3 31.4 - - - +
61A GLU* 3.5 35.7 - - + -
63A THR* 3.5 22.1 - - + +
68A SER* 3.6 5.4 - - - -
69A PRO* 2.6 41.9 + - + +
70A ARG* 3.3 10.2 + - - -
85A VAL 2.9 1.4 + - - -
86A CYS* 1.3 79.6 - - - +
88A GLY* 1.3 57.2 + - - +
90A GLN* 3.6 15.0 - - - -
91A THR* 2.8 35.3 + - - -
529A CIT 3.3 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 4.6 1.1 - - - -
56A LEU* 3.6 29.7 - - - +
57A SER 3.1 17.6 + - - -
84A GLY* 3.7 7.9 - - - -
85A VAL 3.0 7.1 + - - -
87A TYR* 1.3 77.6 - - - +
89A MET* 1.3 59.0 + - - +
91A THR* 3.5 9.3 - - - +
92A MET* 3.3 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLY* 3.6 12.9 - - - +
86A CYS 2.9 11.2 + - - +
88A GLY* 1.3 77.0 - - - +
90A GLN* 1.3 59.1 + - - +
92A MET* 3.2 8.0 + - - +
93A ALA* 3.0 25.5 + - - +
147A VAL* 4.2 14.6 - - + -
165A PHE* 3.4 31.2 - - + +
166A ALA 4.7 0.4 - - - +
168A MET* 3.7 34.6 - - + +
177A GLY* 3.3 28.7 - - - +
178A VAL 3.6 16.4 - - - +
179A GLN* 3.7 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU 5.5 0.5 - - - +
63A THR* 4.2 10.4 + - + +
86A CYS 3.0 16.1 + - - +
87A TYR* 3.6 21.0 - - + +
89A MET* 1.3 80.7 - - - +
91A THR* 1.3 61.5 + - - +
93A ALA* 3.4 7.1 + - - +
94A MET* 3.1 26.0 + - - +
100A VAL* 3.7 9.3 - - + +
143A HIS* 4.5 1.4 - - - +
144A GLY* 4.3 8.0 + - - +
145A ASP* 2.9 51.4 + - - +
147A VAL* 3.7 19.0 - - + +
179A GLN* 3.3 21.1 + - - +
529A CIT 5.2 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 4.4 14.1 - - + -
56A LEU* 4.4 10.8 - - + -
63A THR* 3.8 15.6 - - - +
69A PRO 4.0 0.7 + - - -
70A ARG* 3.2 22.2 - - - -
71A ALA* 4.7 0.7 - - + +
76A PHE* 5.2 0.2 - - + -
87A TYR* 2.8 21.4 + - + +
88A GLY* 3.5 19.1 - - - +
90A GLN* 1.3 75.0 - - - +
92A MET* 1.3 65.7 + - - +
94A MET* 4.3 2.2 - - - -
95A GLN* 2.8 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 4.8 0.9 - - + -
76A PHE* 3.8 28.0 - - + -
82A VAL* 3.5 37.2 - - + +
84A GLY* 4.3 5.2 - - - +
88A GLY 3.3 15.9 - - - +
89A MET 3.2 5.7 + - - +
91A THR* 1.3 79.5 - - - +
93A ALA* 1.3 65.6 + - - +
96A LEU* 3.3 33.5 + - + +
151A PRO* 4.3 0.3 - - - +
154A PHE* 4.0 12.8 - - + -
168A MET* 3.7 20.2 - - + -
175A PHE* 3.9 11.9 - - + -
176A TYR 3.8 27.1 - - - +
177A GLY* 4.4 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A MET* 3.0 12.6 + - - +
90A GLN* 3.5 12.3 - - - +
91A THR 3.3 0.2 - - - -
92A MET* 1.3 80.5 - - - +
94A MET* 1.3 58.7 + - - +
96A LEU 3.2 4.5 + - - -
97A GLY 3.2 0.3 + - - -
98A GLY* 2.7 34.0 + - - -
100A VAL* 4.6 5.4 - - + -
147A VAL* 4.6 18.8 - - + -
149A ALA 4.6 0.7 - - - +
151A PRO* 3.6 13.2 - - + +
168A MET* 3.8 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 3.8 25.6 - - - +
64A THR* 5.5 2.2 - - - -
70A ARG* 4.7 13.7 - - - +
90A GLN 3.1 16.9 + - - +
91A THR* 3.8 6.3 - - - +
93A ALA* 1.3 80.3 - - - +
95A GLN* 1.3 62.6 + - - +
96A LEU 3.1 1.7 + - - -
97A GLY* 3.4 7.4 + - - -
98A GLY 3.2 29.6 - - - +
99A HIS* 3.5 21.3 - - + -
100A VAL* 3.6 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 3.5 22.8 - - - +
71A ALA* 2.9 42.5 + - - +
73A GLN* 3.3 33.8 + - - +
76A PHE* 3.6 21.0 - - + -
91A THR* 2.8 39.8 + - - +
92A MET 4.4 0.4 - - - +
94A MET* 1.3 71.2 - - - +
96A LEU* 1.3 64.5 + - - +
97A GLY 3.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN* 4.3 4.9 - - - +
76A PHE* 4.1 29.2 - - + -
92A MET* 3.3 26.8 + - + +
93A ALA 3.2 2.9 + - - -
94A MET 3.1 1.0 - - - -
95A GLN* 1.3 85.0 - - - +
97A GLY* 1.3 57.8 + - - +
98A GLY 3.8 0.4 - - - -
151A PRO* 3.5 21.4 - - + +
152A SER 5.1 0.5 + - - -
153A ASP* 5.1 1.5 - - - +
154A PHE* 3.9 28.9 - - + -
175A PHE* 4.1 16.8 - - + -
----------------------------------------------------------
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