Contacts of the helix formed by residues 122 - 138 (chain A) in PDB entry 2WH6
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 PRO 122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A SER 3.2 7.3 - - - +
121A THR* 1.3 91.3 - - + +
123A TYR* 1.3 66.6 + - - +
124A TYR* 3.8 28.9 - - + +
125A VAL* 3.0 28.5 + - + +
126A VAL* 3.3 8.4 + - - +
1163A BR 4.5 3.8 - - + -
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Residues in contact with TYR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A HIS* 3.8 11.7 - - - -
27A PRO* 4.3 16.0 + - + +
28A VAL* 3.6 18.7 - - + +
31A LEU* 4.4 13.7 - - - +
121A THR 3.4 2.9 + - - -
122A PRO* 1.3 72.0 - - - +
124A TYR* 1.3 69.7 + - + +
125A VAL 3.1 0.5 + - - -
126A VAL* 3.1 9.0 + - - +
127A ASP* 2.9 49.7 + - + +
1163A BR 3.7 15.6 - - + +
1167A BR 3.8 25.8 - - + -
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Residues in contact with TYR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PRO* 3.2 22.6 - - + +
123A TYR* 1.3 86.8 - - + +
125A VAL* 1.3 78.2 + - + +
127A ASP* 4.1 4.5 - - - -
128A LEU* 2.9 43.0 + - + +
1159A BR 4.0 26.7 - - + -
1163A BR 3.2 29.5 - - + +
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 3.9 25.8 - - + -
79A VAL* 4.6 8.2 - - + +
115A LEU* 3.8 21.3 - - + -
121A THR* 4.0 7.9 - - + -
122A PRO* 3.0 21.7 + - + +
124A TYR* 1.3 109.2 - - + +
126A VAL* 1.3 65.3 + - - +
128A LEU* 4.5 2.1 - - - +
129A SER* 2.8 31.2 + - - -
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A HIS* 3.7 46.4 - - + +
28A VAL* 4.2 6.7 - - + -
115A LEU* 4.0 24.9 - - + +
116A CYS* 4.1 16.4 - - - -
121A THR* 3.6 27.4 - - + +
122A PRO 3.7 6.7 - - - +
123A TYR 3.1 5.1 + - - +
125A VAL* 1.3 77.6 - - - +
127A ASP* 1.3 63.1 + - - +
129A SER* 3.3 1.0 + - - -
130A VAL* 2.9 31.3 + - + +
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Residues in contact with ASP 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 3.5 21.7 - - + +
31A LEU* 4.7 4.6 - - - +
123A TYR* 2.9 49.3 + - + +
124A TYR* 3.8 5.8 - - - +
126A VAL* 1.3 77.8 - - - +
128A LEU* 1.3 62.6 + - + +
130A VAL* 3.9 0.9 - - - +
131A ARG* 2.8 63.9 + - - +
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A HIS* 6.1 0.2 - - - -
79A VAL* 4.0 16.4 - - + -
80A ASP* 3.5 39.5 - - - +
124A TYR* 2.9 30.1 + - + +
125A VAL 4.5 0.4 - - - +
127A ASP* 1.3 80.3 - - + +
129A SER* 1.3 58.6 + - - +
131A ARG* 4.5 15.0 - - - -
132A GLY* 2.8 23.7 + - - -
1159A BR 4.0 23.8 - - + -
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Residues in contact with SER 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP* 3.9 7.8 - - - -
73A ILE* 4.0 4.2 - - - +
79A VAL* 3.2 16.0 - - - +
83A PHE* 3.6 19.9 - - - -
115A LEU* 3.3 29.4 - - - +
125A VAL 2.8 22.8 + - - -
126A VAL 3.7 0.7 - - - -
128A LEU* 1.3 75.7 - - - +
130A VAL* 1.3 61.9 + - - +
132A GLY 3.2 0.2 + - - -
133A MET* 2.9 35.3 + - - +
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 5.1 0.4 - - + -
13A CYS* 6.3 1.1 - - - -
28A VAL* 3.7 25.1 - - + -
29A LEU* 4.2 17.5 - - + -
32A ALA* 4.4 6.7 - - + -
112A CYS* 3.9 31.0 - - + -
115A LEU* 5.3 0.9 - - + -
116A CYS* 5.6 0.2 - - - -
126A VAL* 2.9 27.2 + - + +
129A SER* 1.3 73.3 - - - +
131A ARG* 1.3 68.6 + - + +
133A MET* 3.2 12.9 - - + +
134A LEU* 3.0 42.9 + - + +
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Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 5.8 2.0 - - + -
31A LEU* 3.5 41.2 - - + +
32A ALA* 6.2 1.8 - - + -
35A GLU* 5.7 2.4 - - - +
80A ASP* 5.2 5.2 - - + +
127A ASP* 2.8 41.2 + - - +
128A LEU* 4.0 15.0 - - - +
130A VAL* 1.3 80.5 - - + +
132A GLY* 1.3 56.1 + - - +
134A LEU* 3.8 0.5 - - - +
135A GLU* 2.9 43.1 + - - +
1168A GOL 3.1 48.3 + - - +
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Residues in contact with GLY 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP* 3.9 26.8 - - - +
83A PHE* 3.6 10.4 - - - +
128A LEU 2.8 19.2 + - - -
129A SER 3.7 1.1 - - - -
130A VAL 3.2 0.2 - - - -
131A ARG* 1.3 77.3 - - - +
133A MET* 1.3 56.5 + - - +
135A GLU* 4.0 4.1 - - - +
136A ALA* 3.0 32.6 + - - +
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Residues in contact with MET 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 4.2 7.6 - - + -
13A CYS* 4.3 10.8 - - - -
83A PHE* 3.7 29.7 - - + -
104A TRP* 4.3 1.6 - - - -
108A CYS* 3.5 53.8 - - + +
111A ALA* 4.1 4.5 - - + -
112A CYS* 4.0 23.3 - - + +
129A SER* 2.9 25.6 + - - +
130A VAL* 3.2 19.3 - - + +
132A GLY* 1.3 76.5 - - - +
134A LEU* 1.3 66.3 + - + +
136A ALA* 4.1 0.7 - - - +
137A SER* 2.7 34.6 + - - -
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 3.7 41.7 - - + +
9A LEU* 4.0 17.0 - - + -
10A LEU* 3.8 25.6 - - + +
13A CYS* 5.9 1.3 - - - -
32A ALA* 3.8 21.3 - - + -
130A VAL* 3.0 39.2 + - + +
131A ARG 3.8 2.5 - - - +
133A MET* 1.3 82.7 - - + +
135A GLU* 1.3 63.0 + - - +
137A SER* 3.4 11.7 + - - -
138A GLU* 3.5 15.1 + - - +
1168A GOL 3.9 18.2 - - - +
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Residues in contact with GLU 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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6A ARG* 5.3 0.2 - - - +
80A ASP* 5.1 8.1 - - - +
84A ASN* 4.9 2.6 - - - +
131A ARG* 2.9 27.7 + - - +
132A GLY* 4.1 5.0 - - - +
134A LEU* 1.3 74.6 - - - +
136A ALA* 1.3 66.1 + - - +
138A GLU* 3.3 36.0 + - - +
139A GLY 4.5 0.3 + - - -
1168A GOL 2.7 32.9 + - - +
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Residues in contact with ALA 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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83A PHE 4.1 8.7 - - - +
84A ASN* 3.7 25.5 + - - +
87A PHE* 3.6 27.7 - - + -
104A TRP* 3.9 19.7 - - + -
132A GLY 3.0 18.8 + - - +
135A GLU* 1.3 76.5 - - - +
137A SER* 1.3 63.6 + - - +
139A GLY* 3.0 13.7 + - - -
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Residues in contact with SER 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 THR* 3.4 38.4 - - - +
6A ARG 5.2 0.2 - - - -
9A LEU* 3.4 17.7 - - - +
87A PHE* 4.2 2.9 - - - -
104A TRP* 2.8 29.5 + - - +
133A MET 2.7 21.9 + - - -
134A LEU* 3.7 6.7 - - - -
135A GLU 3.1 0.4 - - - -
136A ALA* 1.3 72.6 - - - +
138A GLU* 1.3 61.0 + - - +
139A GLY 2.9 5.8 - - - -
140A LEU* 2.9 13.7 + - - +
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Residues in contact with GLU 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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5A THR* 4.9 1.6 - - - -
6A ARG* 3.2 47.3 + - + +
134A LEU 3.5 7.6 + - - +
135A GLU* 3.5 29.7 - - - +
136A ALA 3.1 0.8 + - - -
137A SER* 1.3 77.9 - - - +
139A GLY* 1.3 61.4 + - - +
140A LEU 3.0 1.8 + - - -
141A ASP* 3.1 34.5 + - - +
142A GLY 4.8 0.3 + - - -
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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
------------------------------------------------------------
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