Contacts of the helix formed by residues 128 - 141 (chain A) in PDB entry 2Q1V
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 THR 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A TRP* 3.8 0.9 - - - -
126A GLN 4.2 6.5 - - - +
127A VAL* 1.3 78.4 - - - +
129A TYR* 1.3 59.7 + - - +
130A GLU* 3.4 9.5 + - - +
131A GLU* 2.8 47.8 + - - +
132A PHE* 2.9 25.6 + - - +
169A ALA 5.1 3.1 + - - +
183A ARG* 4.7 1.8 - - - +
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Residues in contact with TYR 129 (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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6A GLU* 3.9 28.7 + - + -
9A GLU* 3.2 31.6 - - + +
79A TRP* 3.5 39.3 - + + -
128A THR* 1.3 74.0 - - - +
130A GLU* 1.3 62.0 + - + +
132A PHE* 3.4 10.6 + + - +
133A LEU* 3.0 63.0 + - + +
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Residues in contact with GLU 130 (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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2A ILE* 3.6 38.0 - - + +
6A GLU* 4.0 14.0 - - - +
128A THR* 3.2 7.1 + - - +
129A TYR* 1.3 77.8 - - + +
131A GLU* 1.3 65.6 + - - +
133A LEU* 3.3 3.4 + - - +
134A CYS* 3.1 28.1 + - - -
169A ALA* 3.9 28.5 - - + +
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Residues in contact with GLU 131 (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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127A VAL* 3.5 8.1 - - + +
128A THR* 2.8 48.6 + - + +
130A GLU* 1.3 74.1 - - - +
132A PHE* 1.3 58.6 - - - +
134A CYS* 3.3 2.9 + - - +
135A MET* 2.9 36.0 + - - +
166A LEU* 4.1 8.7 - - + -
169A ALA* 4.1 19.4 - - + +
170A ILE* 4.0 11.1 - - + +
183A ARG* 2.7 49.1 + - - +
187A LEU* 3.6 23.0 - - + +
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Residues in contact with PHE 132 (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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9A GLU* 4.1 10.3 - - - -
75A PHE* 3.6 33.4 - + - -
76A SER* 4.0 9.4 - - - -
79A TRP* 3.4 68.4 - + + -
122A PHE* 4.2 4.9 - + - -
127A VAL* 3.8 7.3 - - + +
128A THR 2.9 16.2 + - - +
129A TYR* 3.5 16.8 - + - +
131A GLU* 1.3 78.4 - - - +
133A LEU* 1.3 62.9 + - + +
135A MET* 3.3 6.1 + - - +
136A LYS* 2.9 57.1 + - + +
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Residues in contact with LEU 133 (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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2A ILE* 4.1 7.6 - - + -
5A LEU* 4.1 20.1 - - + +
6A GLU* 3.4 43.1 - - + +
9A GLU* 3.5 36.1 - - + +
46A TRP* 5.3 0.2 - - - -
129A TYR* 3.0 47.4 + - + +
130A GLU* 3.7 3.8 - - - +
131A GLU 3.3 0.2 - - - -
132A PHE* 1.3 80.6 - - + +
134A CYS* 1.3 63.8 + - - +
136A LYS* 3.4 9.2 + - - +
137A VAL* 3.4 23.7 + - - +
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Residues in contact with CYS 134 (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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2A ILE* 4.1 13.7 - - - -
5A LEU* 4.1 8.1 - - - -
130A GLU 3.1 17.8 + - - +
131A GLU 3.8 5.8 - - - +
133A LEU* 1.3 76.2 - - - +
135A MET* 1.3 65.1 + - - +
137A VAL* 3.1 16.5 + - - +
138A LEU* 3.2 16.8 + - - +
162A TYR* 4.5 6.6 - - - +
165A GLU* 3.6 43.7 - - - -
166A LEU* 3.9 22.9 - - + +
169A ALA* 4.4 4.3 - - - -
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Residues in contact with MET 135 (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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75A PHE* 3.7 19.5 - - + -
127A VAL* 4.6 6.1 - - - -
131A GLU* 2.9 28.7 + - - +
132A PHE 3.6 4.9 - - - +
134A CYS* 1.3 76.6 - - - +
136A LYS* 1.3 63.4 + - - +
138A LEU* 3.1 19.5 + - - +
139A LEU* 3.1 15.6 + - - +
166A LEU* 4.0 19.3 - - + -
187A LEU* 3.2 52.7 - - + +
190A LEU* 3.8 25.1 - - + -
191A LEU* 3.7 20.8 - - + +
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Residues in contact with LYS 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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9A GLU* 2.9 41.5 + - - -
10A PRO* 4.7 2.0 - - - +
46A TRP* 3.4 29.8 - - + +
72A LEU* 3.4 36.2 - - + +
75A PHE* 3.8 16.7 - - + -
76A SER* 3.3 23.1 - - - +
132A PHE* 2.9 37.0 + - + +
133A LEU* 3.7 8.6 + - - +
134A CYS 3.2 0.4 - - - -
135A MET* 1.3 75.9 - - - +
137A VAL* 1.3 62.6 + - - +
139A LEU* 3.1 12.0 + - + +
140A LEU 3.4 0.2 + - - -
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Residues in contact with VAL 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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5A LEU* 4.0 13.2 - - + -
46A TRP* 4.0 14.1 - - + -
50A LEU* 3.8 36.3 - - + -
133A LEU 3.4 14.6 + - - +
134A CYS 3.1 7.2 + - - +
136A LYS* 1.3 76.2 - - - +
138A LEU* 1.3 64.6 + - - +
140A LEU* 3.0 17.7 + - - +
141A LEU* 3.3 15.2 + - + +
158A MET* 6.0 0.7 - - - -
162A TYR* 3.6 42.4 - - + -
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Residues in contact with LEU 138 (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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134A CYS 3.2 13.2 + - - +
135A MET* 3.1 10.2 + - - +
137A VAL* 1.3 77.6 - - - +
139A LEU* 1.3 57.7 + - - +
141A LEU* 3.0 14.4 + - + +
142A SER* 2.6 28.5 + - - +
159A ARG* 4.1 14.4 - - + +
162A TYR* 3.9 27.4 - - + +
163A ILE* 3.7 28.5 - - + -
166A LEU* 4.0 22.0 - - + -
191A LEU* 3.9 27.8 - - + -
244A PHE* 4.3 12.1 - - + -
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Residues in contact with LEU 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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68A SER* 3.5 16.7 - - - -
71A SER* 3.7 30.2 + - - +
72A LEU* 4.1 9.4 - - + -
75A PHE* 3.2 49.6 - - + -
135A MET 3.1 15.4 + - - +
136A LYS* 3.4 9.0 - - - +
137A VAL 3.1 0.4 - - - -
138A LEU* 1.3 76.9 - - - +
140A LEU* 1.3 61.7 + - - +
141A LEU 3.2 0.7 + - - -
142A SER* 3.3 19.5 + - - +
143A THR* 4.4 2.3 + - - -
191A LEU* 3.6 26.7 - - + +
194A MET* 4.1 15.9 - - + -
195A HIS* 6.4 1.6 - - + -
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Residues in contact with LEU 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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46A TRP* 3.9 9.6 - - + -
47A ALA* 4.3 5.4 - - + -
50A LEU* 3.5 31.6 - - + -
53A PHE* 3.9 24.9 - - + -
64A LEU* 3.6 37.9 - - + +
65A ILE* 4.3 11.2 - - + +
68A SER* 3.5 22.0 + - - +
72A LEU* 4.0 18.7 - - + +
136A LYS 3.4 5.1 + - - +
137A VAL* 3.0 13.8 + - + +
139A LEU* 1.3 77.3 - - - +
141A LEU* 1.3 65.9 + - + +
142A SER 3.9 0.3 + - - -
143A THR 5.1 0.9 + - - +
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Residues in contact with LEU 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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53A PHE* 5.1 0.4 - - + -
64A LEU* 4.0 8.1 - - + -
137A VAL* 3.5 27.6 - - + +
138A LEU* 3.0 12.5 + - - +
140A LEU* 1.3 95.5 - - + +
142A SER* 1.3 56.1 + - - +
143A THR 3.8 1.3 - - - -
144A VAL* 4.9 0.9 - - - -
155A PHE* 3.3 32.7 - - + -
158A MET* 3.3 51.4 - - + -
159A ARG* 2.9 44.5 + - + +
162A TYR* 4.4 4.0 - - + -
242A LEU* 3.5 2.1 - - - +
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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