Contacts of the helix formed by residues 135 - 144 (chain A) in PDB entry 6GHM
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 GLY 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ASP* 3.9 3.6 - - - -
96A ARG 4.6 2.2 - - - -
100A SER* 5.8 0.4 - - - -
131A ASN 4.3 1.2 + - - -
132A ARG 5.0 0.8 + - - -
133A ILE 3.4 4.2 + - - -
134A TYR* 1.3 80.1 - - - +
136A PHE* 1.3 59.3 + - - +
137A TYR 3.3 2.0 - - - -
138A ASP* 3.1 16.2 + - - +
139A GLU* 2.9 30.5 + - - +
142A ARG* 5.3 0.5 + - - -
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Residues in contact with PHE 136 (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 VAL* 3.8 20.6 - - + -
95A ASP* 2.7 25.9 + - - +
100A SER* 3.7 26.7 - - - -
101A LEU* 3.6 22.0 - - + -
104A ILE* 4.4 0.9 - - + -
131A ASN* 3.6 22.8 + - + -
135A GLY* 1.3 73.0 - - - +
137A TYR* 1.3 61.5 + - - +
139A GLU* 3.3 5.5 + - + -
140A CYS* 2.9 43.7 + - - -
149A TRP* 3.8 13.5 - + - -
152A PHE* 3.6 45.3 - + + -
156A PHE* 4.0 10.3 - + - -
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Residues in contact with TYR 137 (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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131A ASN 2.9 20.0 + - - +
132A ARG* 3.3 62.9 + - - +
135A GLY 3.3 0.2 - - - -
136A PHE* 1.3 76.2 - - - +
138A ASP* 1.3 70.6 + - - +
140A CYS* 3.4 2.1 + - - +
141A LYS* 2.9 49.5 + - + +
146A ILE* 3.5 33.6 - - + +
149A TRP* 3.6 40.7 - + - +
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Residues in contact with ASP 138 (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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132A ARG* 4.8 7.7 + - - +
133A ILE* 5.0 4.7 - - - +
135A GLY* 3.1 19.4 + - - +
137A TYR* 1.3 96.4 - - - +
139A GLU* 1.3 56.8 + - - +
141A LYS* 3.3 7.2 + - - +
142A ARG* 2.8 48.6 + - - +
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Residues in contact with GLU 139 (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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97A GLY 3.9 4.5 - - - +
98A LYS 3.3 21.2 - - - +
100A SER* 3.2 29.2 + - - -
101A LEU* 2.9 32.8 + - + +
135A GLY 2.9 16.6 + - - +
136A PHE* 3.3 9.4 + - + +
138A ASP* 1.3 75.0 - - - +
140A CYS* 1.3 63.0 + - - +
142A ARG* 3.2 18.1 + - - +
143A ARG* 3.0 57.3 + - - +
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Residues in contact with CYS 140 (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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101A LEU* 4.2 14.8 - - - -
136A PHE* 2.9 56.6 + - - +
137A TYR 3.7 3.4 - - - +
139A GLU* 1.3 76.3 - - - +
141A LYS* 1.3 55.4 + - - +
144A TYR* 2.7 32.8 + - - +
145A ASN 3.1 14.7 + - - +
148A LEU* 5.0 3.8 - - + -
149A TRP* 3.7 31.4 - - + +
152A PHE* 4.2 5.4 - - - -
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Residues in contact with LYS 141 (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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137A TYR* 2.9 41.3 + - + +
138A ASP* 3.7 8.1 - - - +
140A CYS* 1.3 76.4 - - - +
142A ARG* 1.3 64.1 + - - +
144A TYR 3.3 14.2 - - - +
145A ASN* 4.2 7.2 + - - -
146A ILE* 3.6 32.1 - - + +
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Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A LYS 5.8 0.4 + - - -
135A GLY 5.3 0.4 + - - -
138A ASP* 2.8 39.2 + - - +
139A GLU* 3.5 31.5 + - - +
141A LYS* 1.3 80.5 - - - +
143A ARG* 1.3 69.4 + - + +
144A TYR 4.7 0.5 - - - +
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Residues in contact with ARG 143 (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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27A ASN* 3.0 32.6 + - - +
28A VAL 3.5 18.2 + - - -
29A GLN* 4.4 5.7 + - - -
98A LYS 4.6 5.1 + - - -
99A GLN* 4.7 0.2 - - - +
101A LEU* 4.0 12.3 - - + +
102A GLU* 2.8 42.8 + - - -
139A GLU* 3.0 42.1 + - + +
142A ARG* 1.3 89.1 - - + +
144A TYR* 1.3 88.8 + - + +
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Residues in contact with TYR 144 (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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28A VAL 4.6 4.5 + - - -
29A GLN* 4.6 4.0 + - - -
30A LEU* 2.5 35.9 + - - +
32A GLU* 3.8 32.5 - - + -
35A ILE* 3.4 19.5 - - + +
101A LEU* 3.6 31.2 - - + -
140A CYS* 2.7 16.7 + - - +
141A LYS 3.3 10.4 - - - +
142A ARG 4.7 0.9 - - - +
143A ARG* 1.3 91.1 + - + +
145A ASN* 1.3 71.2 + - - +
148A LEU* 3.6 23.8 - - + -
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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