Contacts of the helix formed by residues 84 - 100 (chain A) in PDB entry 4Q96
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 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A VAL* 3.6 30.7 - - + +
42A SER* 6.2 1.1 - - - -
44A TRP* 4.3 17.5 - - + -
45A HIS* 3.6 28.6 - - + +
80A GLU 4.2 0.2 - - - +
81A PHE* 3.0 15.6 + - + +
83A SER* 1.3 94.4 - - - +
85A LEU* 1.3 59.9 + - - +
86A VAL 3.3 2.5 - - - -
87A ASP* 3.3 10.4 + - - +
88A ALA* 2.9 25.3 + - - +
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TRP* 4.3 24.5 - - + -
60A LEU* 4.7 2.2 - - + -
63A ALA* 4.8 2.9 - - + -
67A ILE* 3.9 7.4 - - + -
81A PHE* 3.0 28.0 + - + +
82A GLU 4.0 1.4 + - - -
83A SER 3.9 0.2 - - - -
84A VAL* 1.3 74.7 - - - +
86A VAL* 1.3 65.5 + - - +
88A ALA* 4.0 2.5 - - + -
89A PHE* 2.9 48.5 + - + -
111B TRP* 3.8 20.2 - - + -
117B TYR* 3.5 40.8 - - + +
121B PHE* 3.8 9.4 - - + -
125B LEU* 3.5 14.5 - - + +
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU 5.0 1.3 + - - +
83A SER 5.5 0.4 - - - -
84A VAL 3.3 1.2 - - - -
85A LEU* 1.3 79.2 - - - +
87A ASP* 1.3 65.2 + - - +
90A SER* 3.0 28.8 + - - -
121B PHE* 3.8 25.9 - - + -
124B GLN* 3.9 29.4 - - + +
125B LEU* 3.9 12.1 - - + -
128B SER* 3.5 19.8 + - - -
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A HIS* 3.9 19.8 + - + +
49A ARG* 5.1 4.0 + - - +
84A VAL* 3.3 11.2 + - - +
86A VAL* 1.3 81.0 - - - +
88A ALA* 1.3 66.0 + - - +
90A SER* 3.3 7.5 + - - -
91A HIS* 2.9 25.5 + - - +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TRP* 4.0 19.5 - - + -
45A HIS* 4.0 8.2 + - - +
48A LEU* 3.8 23.8 - - + -
60A LEU* 4.4 5.8 - - + -
84A VAL 2.9 17.2 + - - +
85A LEU* 3.7 10.3 - - + +
86A VAL 3.3 0.2 - - - -
87A ASP* 1.3 76.1 - - - +
89A PHE* 1.3 57.7 + - - +
91A HIS* 3.3 5.0 + - - +
92A VAL* 3.0 33.8 + - - +
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Residues in contact with PHE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.2 23.1 - - + -
85A LEU* 2.9 36.9 + - + +
88A ALA* 1.3 73.6 - - - +
90A SER* 1.3 67.6 + - - +
92A VAL* 3.9 4.4 - - - +
93A ALA* 2.9 28.5 + - - +
104B LEU* 4.3 15.7 - - + +
107B LEU* 4.0 17.5 - - + -
108B LEU* 3.5 33.7 - - + -
111B TRP* 3.6 34.1 - + - -
125B LEU* 3.8 11.7 - - + +
128B SER* 3.4 17.7 - - - +
129B MET* 4.3 19.7 - - + -
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 3.0 19.7 + - - -
87A ASP* 3.6 8.7 - - - -
88A ALA 3.2 0.2 - - - -
89A PHE* 1.3 76.5 - - - +
91A HIS* 1.3 57.6 + - - +
93A ALA* 3.8 1.6 - - - +
94A ARG* 2.9 34.5 + - - +
128B SER* 3.5 21.5 + - - +
131B ASP 3.5 22.1 + - - +
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Residues in contact with HIS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A HIS* 5.7 0.2 - - - +
48A LEU* 4.3 7.4 - - + -
49A ARG* 3.4 60.1 + - + +
56A LYS* 2.9 35.8 + - + -
87A ASP 2.9 17.7 + - - +
88A ALA* 3.5 4.7 - - - +
90A SER* 1.3 77.9 - - - +
92A VAL* 1.3 70.8 + - + +
94A ARG* 3.3 9.7 + - - +
95A GLU* 3.1 54.4 + - + +
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.9 28.9 - - + -
56A LYS* 4.1 24.8 - - + +
57A LEU* 4.9 1.8 - - - +
60A LEU* 3.9 20.6 - - + -
88A ALA 3.0 17.2 + - - +
89A PHE* 3.9 2.7 - - - +
91A HIS* 1.3 82.1 - - + +
93A ALA* 1.3 57.3 + - - +
95A GLU* 3.8 1.7 - - - +
96A ALA* 2.8 29.5 + - + +
104B LEU* 3.9 28.5 - - + -
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE 2.9 17.3 + - - +
90A SER 3.8 3.1 - - - +
92A VAL* 1.3 75.7 - - - +
94A ARG* 1.3 60.0 + - - +
96A ALA* 3.2 1.8 + - - +
97A ASP* 2.8 37.0 + - - +
101B LYS* 3.6 24.7 - - + -
104B LEU* 4.0 6.8 - - + +
128B SER 4.6 0.2 - - - +
129B MET* 3.8 31.4 - - + +
131B ASP 6.0 0.2 - - - +
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Residues in contact with ARG 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A SER* 2.9 23.2 + - - +
91A HIS* 3.6 10.5 - - - +
93A ALA* 1.3 75.9 - - - +
95A GLU* 1.3 65.2 + - - +
97A ASP* 3.2 8.6 + - - +
98A GLU* 2.9 29.2 + - + +
203A UNX 3.1 31.9 + - - -
131B ASP 5.6 4.2 + - - +
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ARG 5.4 0.5 - - - +
53A SER* 4.3 19.3 + - - -
56A LYS* 3.6 29.1 + - + -
91A HIS* 3.1 39.2 + - + +
92A VAL 3.9 2.7 - - - +
94A ARG* 1.3 79.3 - - + +
96A ALA* 1.3 65.6 + - - +
98A GLU* 3.4 8.0 + - - +
99A GLY* 3.1 19.9 + - - -
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Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 2.8 20.7 + - + +
93A ALA* 3.4 5.8 - - - +
95A GLU* 1.3 77.9 - - - +
97A ASP* 1.3 61.7 + - - +
99A GLY* 3.9 1.0 - - - -
100A CYS* 3.1 25.0 + - - +
100B CYS* 4.2 17.3 - - + +
101B LYS* 3.9 20.6 - - + -
104B LEU* 4.8 4.7 - - + -
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ALA 2.8 24.2 + - - +
94A ARG* 3.6 7.5 - - - +
96A ALA* 1.3 69.8 - - - +
98A GLU* 1.3 65.9 + - - +
99A GLY 3.4 0.2 + - - -
100A CYS* 3.5 17.5 + - - +
101A LYS 4.9 0.7 + - - -
100B CYS* 5.5 1.6 - - - +
101B LYS* 2.7 38.5 + - - +
129B MET 4.4 5.2 - - - +
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Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ARG* 2.9 18.6 + - + +
95A GLU* 3.6 10.1 - - - +
96A ALA 3.3 0.2 - - - -
97A ASP* 1.3 78.6 - - - +
99A GLY* 1.3 60.0 + - - +
101A LYS 4.9 1.4 + - - -
102A LYS* 3.6 23.6 + - - +
105A GLU* 5.4 2.6 - - - +
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Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLU 3.1 12.3 + - - -
96A ALA 3.9 0.7 - - - -
98A GLU* 1.3 78.8 - - - +
100A CYS* 1.3 65.1 - - - +
101A LYS 3.1 3.6 + - - -
102A LYS* 3.3 33.7 + - - +
1617F PRO* 3.8 15.5 - - - +
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Residues in contact with CYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ALA 3.1 12.8 + - - +
97A ASP* 3.5 13.4 + - - +
98A GLU 3.4 2.0 - - - -
99A GLY* 1.3 77.6 - - - +
101A LYS* 1.3 57.4 + - + +
103A PRO* 3.7 0.3 - - - +
96B ALA* 3.1 28.9 - - - -
97B ASP* 4.2 6.1 - - - +
100B CYS* 2.1 50.7 - - + -
1615F TYR* 2.8 35.2 + - - -
1617F PRO* 3.5 7.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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