Contacts of the helix formed by residues 122 - 142 (chain B) in PDB entry 4WMJ
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 122 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 4.9 1.1 - - + -
106B ALA* 4.0 27.1 - - + -
115B ILE* 2.8 29.9 + - + +
117B VAL* 3.7 32.1 - - + -
120B LYS* 3.8 15.0 - - - +
121B ASP* 1.3 74.8 - - - +
123B THR* 1.3 68.1 + - - +
124B PRO 3.4 0.4 - - - -
125B ASP* 2.9 16.7 + - + +
126B VAL* 3.0 13.8 + - + +
272B TRP* 3.6 31.9 - - + +
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Residues in contact with THR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ALA 5.9 0.7 - - - -
109B ASN* 2.9 23.3 + - - +
112B ASN* 3.7 32.3 - - + +
113B ARG 2.9 6.2 + - - -
115B ILE* 4.1 2.9 + - - +
121B ASP* 2.9 23.5 + - - +
122B VAL* 1.3 77.5 - - - +
124B PRO* 1.4 66.2 - - + +
126B VAL* 3.2 7.5 + - - +
127B ASN* 2.9 43.8 + - - +
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Residues in contact with PRO 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ASP* 3.6 28.3 - - + +
123B THR* 1.4 96.2 - - + +
125B ASP* 1.3 58.9 + - - +
127B ASN* 3.8 6.9 - - + +
128B ALA* 3.0 29.3 + - - +
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Residues in contact with ASP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LYS* 2.6 38.1 + - - +
121B ASP 4.7 1.6 - - - -
122B VAL* 2.9 12.2 + - + +
124B PRO* 1.3 77.9 - - - +
126B VAL* 1.3 67.2 + - + +
128B ALA* 3.4 5.7 + - - +
129B VAL* 3.2 27.9 + - - +
270B TRP* 3.6 28.8 + - + -
272B TRP* 6.1 0.2 - - + -
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ALA 3.5 29.2 - - - +
107B LEU* 3.8 22.4 - - + +
122B VAL* 3.0 22.0 + - + +
123B THR* 3.6 8.1 - - - +
125B ASP* 1.3 76.3 - - - +
127B ASN* 1.3 62.5 + - - +
129B VAL* 3.4 5.0 + - - +
130B LEU* 3.1 37.1 + - + +
270B TRP* 3.7 15.5 - - + -
272B TRP* 3.9 26.0 - - + -
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Residues in contact with ASN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASN 5.2 1.0 - - - +
110B ARG* 5.2 3.3 + - - -
112B ASN* 3.1 36.7 + - - +
123B THR* 2.9 26.2 + - - +
124B PRO* 3.9 6.3 - - + +
126B VAL* 1.3 80.3 - - - +
128B ALA* 1.3 59.4 + - - +
130B LEU* 3.4 17.7 + - - +
131B ALA* 2.9 29.0 + - - +
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PRO 3.0 18.2 + - - +
125B ASP* 3.7 7.4 - - - +
126B VAL 3.3 0.2 - - - -
127B ASN* 1.3 72.6 - - - +
129B VAL* 1.3 68.3 + - + +
131B ALA* 3.3 7.6 + - - +
132B HIS* 3.1 22.6 + - - +
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ASP 3.2 14.5 + - - +
126B VAL 3.8 7.0 - - - +
127B ASN 3.3 0.2 - - - -
128B ALA* 1.3 76.8 - - + +
130B LEU* 1.3 64.0 + - + +
132B HIS* 3.2 8.4 + - + +
133B MET* 2.9 39.5 + - + +
267B PHE* 4.7 5.6 - - + -
268B GLY* 3.6 37.7 - - - +
270B TRP* 3.7 15.5 - - + -
282B ALA* 4.0 19.3 - - + +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU 4.2 8.1 - - - +
110B ARG* 4.0 23.1 - - - +
126B VAL* 3.1 33.8 + - + +
127B ASN* 3.7 16.6 - - - +
129B VAL* 1.3 77.2 - - + +
131B ALA* 1.3 56.1 + - - +
133B MET* 3.3 13.0 + - - -
134B LYS* 2.9 29.5 + - - +
280B TRP 4.8 5.4 - - - +
281B SER 5.9 0.7 - - - -
293B PHE* 3.5 22.5 - - + -
296B PHE* 4.0 18.4 - - + -
300B LEU* 3.8 19.5 - - + -
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASN 2.9 16.3 + - - +
128B ALA* 3.5 9.2 - - - +
129B VAL 3.2 0.2 - - - -
130B LEU* 1.3 76.4 - - - +
132B HIS* 1.3 57.5 + - - +
134B LYS* 3.3 12.2 + - - +
135B GLU* 3.0 29.5 + - - +
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Residues in contact with HIS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ALA 3.1 12.8 + - - +
129B VAL* 3.3 12.7 - - - +
131B ALA* 1.3 74.3 - - - +
133B MET* 1.3 58.6 + - - +
135B GLU* 3.3 15.7 + - + +
136B PHE* 2.9 31.2 + - + +
264B LYS 3.1 27.8 + - - -
265B ASN* 4.7 4.0 + - - -
266B MET 3.8 15.1 + - - -
267B PHE* 3.4 37.0 - + - -
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Residues in contact with MET 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B VAL* 2.9 26.1 + - + +
130B LEU* 3.6 25.1 - - - +
132B HIS* 1.3 74.8 - - - +
134B LYS* 1.3 56.0 + - - +
136B PHE* 4.0 0.3 - - - +
137B SER* 2.6 38.8 + - - +
267B PHE* 3.9 24.2 - - + -
281B SER 3.7 13.5 - - - +
282B ALA* 3.8 19.3 - - - +
284B GLY 3.9 0.7 - - - +
285B LEU* 3.6 41.7 - - + +
288B SER* 4.6 2.9 - - - +
293B PHE* 4.2 7.4 - - + -
296B PHE* 3.8 19.7 - - + -
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Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU 2.9 13.4 + - - +
131B ALA* 3.4 12.6 - - - +
132B HIS 3.2 0.2 - - - -
133B MET* 1.3 76.7 - - - +
135B GLU* 1.3 62.6 + - - +
137B SER* 3.8 0.9 - - - -
138B THR* 3.0 39.0 + - + +
293B PHE* 3.5 44.9 - - + +
294B GLU* 5.8 5.7 - - - +
297B GLU* 5.5 2.6 + - - -
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ALA 3.0 13.9 + - - +
132B HIS* 3.3 18.9 + - + +
134B LYS* 1.3 77.1 - - - +
136B PHE* 1.3 64.5 + - - +
138B THR* 3.0 20.3 + - - +
139B GLN* 3.1 39.3 + - - +
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Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B HIS* 2.9 20.4 + - + +
133B MET 4.0 1.1 - - - +
135B GLU* 1.3 78.4 - - - +
137B SER* 1.3 64.4 + - - +
139B GLN* 3.1 10.0 + - - +
140B VAL* 2.9 45.2 + - + +
145B TRP* 3.6 44.2 - + - -
208B LEU* 3.9 18.4 - - + -
247B VAL* 3.8 23.6 - - + -
265B ASN* 4.9 4.7 - - - -
267B PHE* 3.6 26.9 - + + -
285B LEU* 4.0 26.5 - - + -
289B LEU* 4.2 8.5 - - + -
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B MET 2.6 26.4 + - - -
134B LYS* 3.8 4.3 - - - -
136B PHE* 1.3 75.8 - - - +
138B THR* 1.3 65.7 + - - +
140B VAL* 3.3 0.5 + - - +
141B ILE* 2.9 35.0 + - - +
285B LEU* 4.0 6.6 - - - +
288B SER* 2.8 41.0 + - - -
289B LEU* 3.7 13.7 + - - +
293B PHE* 4.6 6.5 - - - -
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Residues in contact with THR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LYS* 3.0 27.0 + - + +
135B GLU* 3.0 17.5 + - - +
137B SER* 1.3 77.6 - - - +
139B GLN* 1.3 57.3 + - - +
141B ILE* 4.0 6.0 - - + +
142B SER* 2.9 37.0 + - - -
293B PHE* 5.4 5.6 - - + -
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Residues in contact with GLN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B GLU* 3.1 40.2 + - + +
136B PHE* 3.1 14.0 + - - +
138B THR* 1.3 76.4 - - - +
140B VAL* 1.3 66.1 + - - +
142B SER* 3.2 5.8 + - - -
144B ALA* 3.1 20.0 + - + -
145B TRP* 2.9 57.3 + - + +
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 2.9 51.8 + - + +
139B GLN* 1.3 75.2 - - - +
141B ILE* 1.3 68.3 + - - +
143B GLY* 3.3 12.1 + - - -
145B TRP* 4.0 17.6 - - + +
153B ILE* 4.1 32.8 + - + +
156B VAL* 4.9 0.7 - - + -
181B HIS* 5.0 0.3 + - - -
182B LEU* 4.1 12.1 - - + +
208B LEU* 4.0 17.0 - - + -
289B LEU* 3.6 22.2 - - + -
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B SER* 2.9 28.3 + - - +
138B THR* 4.0 5.6 - - + +
140B VAL* 1.3 76.8 - - - +
142B SER* 1.3 62.8 + - - +
143B GLY* 3.3 0.9 + - - -
180B ASN* 3.5 22.7 - - + +
181B HIS* 3.0 38.0 + - + +
182B LEU* 3.9 9.0 - - + -
288B SER 3.9 13.5 - - - +
289B LEU* 3.4 29.6 - - + +
292B GLY* 4.0 11.4 - - - -
293B PHE 5.1 0.2 - - - +
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Residues in contact with SER 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B THR* 2.9 21.2 + - - -
139B GLN* 3.2 3.5 + - - -
141B ILE* 1.3 78.7 - - - +
143B GLY* 1.3 57.7 + - - +
144B ALA* 3.0 25.6 + - - +
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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
------------------------------------------------------------
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