Contacts of the helix formed by residues 85 - 98 (chain A) in PDB entry 4G98
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 85 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TYR* 3.6 37.5 - - + -
62A GLU* 2.9 4.6 + - - -
81A GLU 5.6 1.2 + - - -
82A GLU 4.2 5.5 + - - -
83A LEU 2.9 18.6 + - - +
84A HIS* 1.3 88.2 + - - +
86A ARG* 1.3 67.5 + - - +
87A ALA 3.4 2.5 - - - -
88A ALA* 3.1 14.2 + - - +
89A LEU* 2.9 23.3 + - + +
137A TYR* 4.0 3.6 - - + -
140A ASP* 4.3 2.9 - - - +
165A ALA 3.4 6.9 + - - -
166A PHE* 2.8 53.3 + - + -
168A THR 2.7 30.5 + - - -
169A PHE* 3.5 33.8 - - - +
170A PRO* 4.6 5.5 - - - +
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Residues in contact with ARG 86 (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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55A TYR* 3.1 26.2 + - + -
58A TYR* 4.7 2.2 - - - +
59A THR* 3.4 42.8 + - - +
62A GLU* 3.0 23.0 + - + +
63A GLU* 5.7 2.8 + - - +
84A HIS* 3.7 0.8 - - + -
85A ARG* 1.3 77.1 - - - +
87A ALA* 1.3 57.9 + - - +
89A LEU* 3.1 11.6 + - - +
90A GLU* 2.9 52.4 + - + +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A HIS 5.3 2.3 + - - +
85A ARG 3.4 0.4 - - - -
86A ARG* 1.3 76.9 - - - +
88A ALA* 1.3 63.5 + - - +
90A GLU* 3.2 18.7 + - - +
91A GLN* 3.1 33.5 + - - +
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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
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84A HIS 5.2 0.8 + - - +
85A ARG* 3.1 28.6 + - - +
87A ALA* 1.3 78.5 - - - +
89A LEU* 1.3 56.1 + - - +
91A GLN* 3.2 13.5 + - - +
92A ASP* 3.0 25.1 + - - -
165A ALA* 3.4 42.0 - - + +
166A PHE* 3.9 3.1 - - - +
168A THR 5.2 0.7 - - - +
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Residues in contact with LEU 89 (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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51A MET* 3.7 38.1 - - + +
54A LEU* 3.6 25.4 - - + +
55A TYR* 3.8 17.7 - - + +
58A TYR* 3.7 27.6 - - + -
85A ARG* 2.9 16.1 + - + +
86A ARG* 3.6 9.0 - - - +
88A ALA* 1.3 73.4 - - - +
90A GLU* 1.3 60.6 + - - +
92A ASP* 3.6 6.2 - - - +
93A MET* 2.8 38.9 + - + +
166A PHE* 3.6 28.7 - - + -
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 3.8 17.2 + - + -
86A ARG* 2.9 56.4 + - - +
87A ALA* 3.2 18.7 + - - +
89A LEU* 1.3 75.1 - - - +
91A GLN* 1.3 63.5 + - + +
93A MET* 3.3 4.3 + - - +
94A ALA* 3.1 22.5 + - - +
101A TRP* 3.9 25.8 + - + -
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Residues in contact with GLN 91 (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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87A ALA* 3.1 25.4 + - - +
88A ALA* 3.4 8.6 - - - +
90A GLU* 1.3 74.4 - - + +
92A ASP* 1.4 59.9 + - - +
94A ALA* 3.2 7.7 + - - +
95A PHE* 3.0 27.8 + - - +
165A ALA* 3.5 22.2 - - + +
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Residues in contact with ASP 92 (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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51A MET* 4.8 4.8 - - + +
88A ALA 3.0 11.9 + - - +
89A LEU* 3.7 10.6 - - + +
91A GLN* 1.4 77.2 - - - +
93A MET* 1.3 68.2 + - + +
95A PHE* 3.2 7.6 + - - +
96A TRP* 2.8 34.8 + - + -
163A GLY* 3.1 26.8 + - - +
164A LEU* 3.7 1.2 - - - -
165A ALA* 2.8 26.5 + - - +
166A PHE* 2.7 36.2 + - - +
167A PHE* 5.3 0.3 - - - -
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Residues in contact with MET 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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51A MET* 3.6 38.4 - - + +
52A ALA* 3.7 21.5 - - - +
55A TYR* 4.3 10.5 - - + -
89A LEU* 2.8 30.5 + - + +
90A GLU 3.7 2.2 - - - +
92A ASP* 1.3 82.4 - - + +
94A ALA* 1.3 53.0 + - - +
96A TRP* 4.4 3.4 - - + +
97A TYR* 2.7 50.1 + - + +
101A TRP* 3.4 41.5 - - + +
105A ILE* 3.7 17.0 - - + -
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Residues in contact with ALA 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 GLU 3.1 12.9 + - - +
91A GLN* 3.2 10.5 + - - +
93A MET* 1.3 73.6 - - - +
95A PHE* 1.3 59.9 + - - +
98A GLY* 2.8 40.1 + - - +
99A PRO* 5.2 2.7 - - + -
101A TRP* 3.6 14.3 - - + +
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Residues in contact with PHE 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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91A GLN 3.0 12.4 + - - +
92A ASP* 3.3 10.8 - - - +
94A ALA* 1.3 79.7 - - - +
96A TRP* 1.3 90.4 + + - +
98A GLY 4.4 1.4 + - - -
157A LEU* 3.8 20.9 - - + -
158A PRO* 5.4 3.1 - - + -
162A GLU* 3.7 24.9 - - + -
163A GLY* 3.3 29.2 - - - +
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Residues in contact with TRP 96 (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 ARG* 3.9 31.6 - - + -
47A PHE* 3.7 21.8 - + - -
48A LYS* 3.4 48.7 + - + +
51A MET* 5.4 4.3 - - + -
92A ASP* 2.8 34.3 + - + +
93A MET* 4.9 5.8 - - + -
95A PHE* 1.3 101.1 - + - +
97A TYR* 1.3 69.0 + - + +
155A MET* 4.3 17.9 - - + -
157A LEU* 3.8 33.9 - - + -
163A GLY 3.0 22.2 + - - -
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Residues in contact with TYR 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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48A LYS* 3.1 65.3 + - + +
49A LEU* 3.9 1.7 + - - +
52A ALA* 4.1 0.2 - - + -
93A MET* 2.7 32.5 + - + +
96A TRP* 1.3 82.8 - - + +
98A GLY* 1.3 59.7 + - - +
100A HIS 4.7 1.6 + - - -
101A TRP* 3.6 19.6 + - + -
104A ALA* 3.9 28.0 - - + +
105A ILE* 3.7 20.2 - - + -
106A PRO* 3.3 32.6 - - + +
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Residues in contact with GLY 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 ALA* 2.8 20.9 + - - -
95A PHE 4.4 1.4 + - - -
96A TRP 3.7 1.4 - - - -
97A TYR* 1.3 77.6 - - - +
99A PRO* 1.3 76.3 - - - +
100A HIS 3.2 2.7 - - - -
101A TRP* 3.2 24.9 + - - +
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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