Contacts of the helix formed by residues 87 - 100 (chain A) in PDB entry 6A08
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 GLU 87 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ARG* 4.4 2.0 - - - -
85A HIS* 3.0 27.3 + - + +
86A PRO* 1.3 80.0 - - + +
88A GLY* 1.3 66.8 + - - +
89A GLU 3.3 0.5 + - - -
90A LEU* 3.0 25.9 + - + +
91A ALA* 3.8 25.4 - - + +
94A ARG* 4.7 12.8 + - - +
111A VAL* 4.6 3.6 - - - +
318A GLN* 4.5 11.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
81A GLN* 3.6 26.5 - - - -
82A ARG* 3.8 7.2 - - - -
85A HIS* 3.0 19.3 + - - +
86A PRO 3.2 0.6 - - - -
87A GLU* 1.3 77.8 - - - +
89A GLU* 1.3 64.1 + - - -
91A ALA* 3.1 13.4 + - - +
92A VAL* 3.4 12.5 + - - +
313A LEU* 3.9 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL 4.7 0.7 - - - +
80A TYR 3.7 2.1 + - - -
81A GLN* 3.0 37.1 + - - +
87A GLU 3.3 0.8 + - - -
88A GLY* 1.3 73.9 - - - -
90A LEU* 1.3 58.1 + - - +
92A VAL* 3.8 1.1 - - - +
93A ALA* 2.9 32.5 + - - +
103A TYR* 3.2 21.2 + - + +
106A CYS* 6.1 1.1 - - + +
109A SER* 3.4 10.3 - - - -
110A SER* 2.7 44.6 + - - -
111A VAL* 3.4 16.7 + - + +
116A ILE* 3.5 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 3.0 14.0 + - + +
89A GLU* 1.3 77.3 - - - +
91A ALA* 1.3 63.5 + - - +
93A ALA* 4.1 2.2 - - - +
94A ARG* 3.0 62.0 + - - +
111A VAL* 4.0 27.1 - - + +
115A GLU* 3.9 22.0 - - + +
116A ILE* 4.0 11.4 - - + -
119A VAL* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 3.6 27.8 + - + +
88A GLY 3.1 10.1 + - - +
90A LEU* 1.3 77.9 - - - +
92A VAL* 1.3 64.4 + - - +
94A ARG* 4.7 1.8 - - - +
95A ALA* 3.2 19.6 + - - +
313A LEU* 3.7 13.9 - - + -
317A GLY* 4.3 0.7 - - - -
318A GLN* 3.5 41.9 - - - +
321A VAL* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 4.1 6.1 - - + -
81A GLN* 3.4 19.1 - - - +
88A GLY 3.7 3.1 - - - +
89A GLU 3.4 2.1 + - - +
90A LEU 3.3 0.2 - - - -
91A ALA* 1.3 78.5 - - - +
93A ALA* 1.3 57.4 + - - +
95A ALA* 3.3 2.8 + - - +
96A ALA* 2.9 27.5 + - - +
103A TYR* 3.4 28.0 - - + -
309A VAL* 3.6 25.6 - - + -
310A MET* 4.2 6.1 - - + -
313A LEU* 3.6 35.0 - - + -
321A VAL* 4.3 13.8 - - + +
----------------------------------------------------------
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 GLU 2.9 17.7 + - - +
90A LEU 4.1 2.2 - - - +
92A VAL* 1.3 77.3 - - - +
94A ARG* 1.3 58.0 + - - +
96A ALA* 3.8 1.1 - - - +
97A ARG* 2.9 30.5 + - - +
103A TYR* 3.9 23.3 - - + +
116A ILE* 3.6 25.6 - - + +
119A VAL* 3.8 16.7 - - + +
120A GLY 5.3 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 4.7 16.6 + - - +
90A LEU* 3.0 56.1 + - - +
91A ALA 3.8 0.7 - - - +
93A ALA* 1.3 77.5 - - - +
95A ALA* 1.3 57.6 + - - +
97A ARG* 3.4 18.1 + - - +
98A ASP* 3.0 34.5 + - - +
119A VAL* 3.7 27.4 - - + +
318A GLN* 3.5 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA 3.2 11.3 + - - +
92A VAL 3.8 0.2 - - - +
94A ARG* 1.3 75.7 - - - +
96A ALA* 1.3 67.3 + - - +
98A ASP* 3.2 7.4 + - - +
99A ALA* 3.0 24.6 + - - +
318A GLN* 3.7 12.9 - - + +
321A VAL* 3.5 35.2 - - + -
322A ARG* 3.7 21.3 - - + +
325A LEU* 3.9 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 4.3 17.3 - - + -
92A VAL 2.9 16.7 + - - +
93A ALA 3.8 3.8 - - - +
95A ALA* 1.3 77.2 - - - +
97A ARG* 1.3 62.5 + - - +
99A ALA 3.1 1.4 + - - -
100A GLY 2.9 19.2 + - - -
101A VAL* 3.0 28.1 + - + +
103A TYR* 4.0 19.3 - - + -
321A VAL* 5.9 0.2 - - + -
325A LEU* 3.9 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA 2.9 18.9 + - - +
94A ARG* 3.5 29.5 + - - +
96A ALA* 1.3 74.4 - - - +
98A ASP* 1.3 93.5 + - - +
100A GLY* 3.1 13.7 + - - -
101A VAL 4.8 1.6 - - - +
119A VAL* 2.9 40.6 + - + +
120A GLY* 4.5 0.7 - - - +
121A GLY* 3.7 33.9 - - - +
318A GLN* 4.7 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG 3.0 19.6 + - - +
95A ALA* 3.7 6.2 - - - +
97A ARG* 1.3 109.5 + - - +
99A ALA* 1.3 60.1 + - - +
100A GLY 3.7 0.3 + - - -
318A GLN* 3.9 13.3 + - - -
322A ARG* 6.1 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 3.3 17.3 - - - +
71A LEU* 5.6 1.4 - - + +
95A ALA 3.0 15.1 + - - +
96A ALA 3.1 2.7 + - - +
98A ASP* 1.3 77.3 - - - +
100A GLY* 1.3 62.0 + - - +
101A VAL* 3.6 9.2 + - + +
322A ARG* 6.2 0.9 - - - -
325A LEU* 3.7 33.4 - - + +
326A GLU* 6.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG 4.7 1.4 - - - +
69A ALA* 3.6 8.5 - - - -
70A ALA* 2.9 30.6 + - - -
96A ALA 2.9 3.4 + - - -
97A ARG* 3.1 12.8 + - - -
98A ASP 3.3 1.0 + - - -
99A ALA* 1.3 80.0 - - - +
101A VAL* 1.3 58.9 + - - +
102A PRO* 4.2 0.5 - - - +
122A ARG* 6.0 4.5 - - - -
----------------------------------------------------------
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