Contacts of the helix formed by residues 126 - 142 (chain B) in PDB entry 1CCW
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 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ALA* 3.3 22.9 - - - +
96B ASP* 3.1 19.0 - - - +
99B THR* 3.7 4.5 - - - +
107B CYS* 4.0 22.7 - - + -
111B ILE* 3.8 17.9 - - + -
122B LEU* 3.9 5.6 - - + -
124B GLY 3.6 8.5 - - - +
125B PHE* 1.3 78.8 - - - +
127B GLY* 1.3 66.1 + - - +
128B VAL 3.3 2.7 - - - -
129B ASN* 3.2 6.7 + - + -
130B PHE* 3.0 39.7 + - + -
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 4.3 6.1 - - - +
99B THR* 4.4 2.0 + - - -
125B PHE* 2.9 31.6 + - - -
126B PRO* 1.3 72.0 - - - +
128B VAL* 1.3 58.3 + - - +
130B PHE 3.5 0.9 + - - -
131B GLY 2.9 22.9 + - - -
135B CYS* 3.9 9.0 - - - -
158B LEU* 4.5 12.6 - - - -
161B ILE* 3.7 12.8 - - - +
162B ILE* 5.3 0.7 - - - -
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TRP* 3.9 12.8 - - + -
26B THR* 2.8 28.4 + - - +
99B THR* 4.3 5.4 - - + +
104B TYR* 3.7 37.9 - - + +
126B PRO 3.3 0.4 - - - -
127B GLY* 1.3 75.7 - - - +
129B ASN* 1.3 65.1 + - - +
131B GLY* 3.2 6.6 + - - -
157B LEU* 3.7 23.8 - - + -
158B LEU* 3.8 41.6 - - + +
161B ILE* 3.7 14.1 - - + +
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Residues in contact with ASN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TRP* 3.8 20.8 + - - +
26B THR* 3.7 10.6 - - - +
99B THR* 4.7 0.3 + - - -
104B TYR* 3.0 37.9 + - - +
107B CYS* 3.1 26.4 - - - +
108B GLU* 2.9 34.1 + - - +
111B ILE* 4.0 13.7 - - + -
126B PRO* 3.2 8.7 + - + +
128B VAL* 1.3 78.2 - - - +
130B PHE* 1.3 61.6 + - - +
131B GLY 3.5 0.3 + - - -
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Residues in contact with PHE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B THR* 4.7 0.7 - - - -
29B GLU* 4.5 1.9 - - - +
70B ALA 2.8 31.0 - - - -
71B LEU* 3.9 3.1 - - + -
72B LEU* 3.6 31.9 - - + -
111B ILE* 4.1 22.4 - - + -
125B PHE* 3.3 41.1 - + + -
126B PRO* 3.0 34.4 + - + +
127B GLY 4.0 3.1 - - - +
129B ASN* 1.3 77.7 - - - +
131B GLY* 1.3 64.0 + - - +
133B LYS* 4.2 2.4 + - - +
134B GLY* 3.1 24.8 + - - -
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Residues in contact with GLY 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B THR* 3.8 13.5 - - - -
29B GLU* 3.6 8.1 - - - -
127B GLY 2.9 11.1 + - - -
128B VAL 3.2 13.0 + - - -
129B ASN 3.3 0.2 - - - -
130B PHE* 1.3 76.6 - - - +
132B VAL* 1.3 67.2 - - - -
133B LYS 3.2 0.2 - - - -
135B CYS* 3.0 26.2 + - - -
161B ILE* 3.5 10.3 - - - -
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B THR 4.8 0.2 - - - +
29B GLU* 2.9 33.2 + - + +
30B VAL* 3.8 28.9 - - + -
131B GLY* 1.3 71.6 - - - -
133B LYS* 1.3 64.9 + - - +
135B CYS* 3.3 2.0 + - - +
136B ARG* 2.9 55.2 + - - +
161B ILE* 3.6 23.0 - - + +
164B ALA* 3.7 19.7 - - + +
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU* 3.0 19.7 + - - +
130B PHE 4.7 2.0 - - - +
132B VAL* 1.3 79.4 - - - +
134B GLY* 1.3 63.4 + - - +
136B ARG* 3.4 7.0 + - - +
137B LYS* 3.1 27.6 + - + +
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Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 3.6 27.7 - - - +
125B PHE* 4.8 0.4 - - - -
130B PHE* 3.1 27.4 + - - -
133B LYS* 1.3 75.4 - - - +
135B CYS* 1.3 66.9 + - - +
137B LYS* 3.0 13.7 + - - +
138B VAL* 3.1 16.4 + - - +
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Residues in contact with CYS 135 (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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125B PHE* 4.1 8.5 - - - -
127B GLY* 3.9 16.2 - - - -
130B PHE* 4.8 0.4 - - - +
131B GLY 3.0 19.9 + - - +
132B VAL 3.8 3.1 - - - +
134B GLY* 1.3 76.5 - - - +
136B ARG* 1.3 60.4 + - - +
138B VAL* 3.2 3.4 + - - +
139B LEU 3.1 11.6 + - - -
161B ILE* 4.1 11.4 - - - +
162B ILE* 4.3 9.2 - - - -
165B GLY* 3.6 16.2 - - - +
167B TRP* 3.0 55.8 + - + +
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Residues in contact with ARG 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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29B GLU 5.9 0.2 + - - -
34B GLU* 2.8 44.2 + - - -
35B ALA* 3.9 6.9 - - - +
38B TYR* 3.5 50.9 - - + +
132B VAL* 2.9 34.2 + - - +
133B LYS* 3.7 7.2 - - - +
135B CYS* 1.3 73.2 - - - +
137B LYS* 1.3 60.9 + - - +
139B LEU* 3.2 1.0 + - - +
140B GLU* 2.8 43.4 + - - +
164B ALA* 2.9 26.4 + - - +
165B GLY* 3.6 18.4 - - - +
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Residues in contact with LYS 137 (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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72B LEU* 3.7 22.6 - - + +
73B ASP* 3.4 28.6 + - - -
76B ILE* 3.7 14.4 - - + -
133B LYS* 3.1 19.3 + - + +
134B GLY* 3.0 11.9 + - - +
136B ARG* 1.3 75.9 - - - +
138B VAL* 1.3 65.0 + - - +
140B GLU* 3.4 9.0 + - - +
141B ALA* 3.0 26.7 + - + +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 3.6 19.7 - - + -
75B HIS* 4.1 11.4 - - + +
76B ILE* 3.9 16.2 - - + -
79B LEU* 3.7 30.1 - - + -
93B SER* 4.5 2.0 - - - +
125B PHE* 3.9 15.7 - - + -
134B GLY 3.1 15.3 + - - +
135B CYS* 3.5 7.9 - - - +
136B ARG 3.1 0.2 - - - -
137B LYS* 1.3 77.6 - - - +
139B LEU* 1.3 64.5 + - - +
141B ALA* 3.1 10.6 + - - +
142B VAL* 3.3 16.4 + - + +
146B LEU* 3.8 14.1 - - + -
167B TRP* 4.5 4.5 - - + -
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Residues in contact with LEU 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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38B TYR* 3.6 26.5 - - + +
42B ILE* 3.8 28.7 - - + -
46B LYS* 2.8 53.4 + - + +
135B CYS 3.1 9.4 + - - +
136B ARG 3.2 5.1 + - - +
138B VAL* 1.3 78.7 - - - +
140B GLU* 1.3 62.4 + - + +
142B VAL* 3.2 9.9 + - - +
144B LEU 4.6 8.1 - - - +
146B LEU* 3.5 26.6 - - + +
165B GLY 4.0 7.6 - - - +
166B GLY* 3.6 17.5 - - - +
167B TRP* 4.4 0.4 - - + -
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Residues in contact with GLU 140 (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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38B TYR* 2.6 36.3 + - - +
46B LYS* 4.1 7.9 + - - +
136B ARG* 2.8 30.2 + - - +
137B LYS* 4.0 7.3 - - - +
139B LEU* 1.3 74.9 - - + +
141B ALA* 1.3 58.0 + - - +
142B VAL 3.3 4.8 + - - +
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Residues in contact with ALA 141 (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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76B ILE* 3.5 33.2 - - + -
80B ARG* 3.0 39.8 + - - +
83B GLN* 5.1 1.6 + - - -
137B LYS* 3.0 18.2 + - + +
138B VAL 3.1 4.4 + - - +
140B GLU* 1.3 78.9 - - - +
142B VAL* 1.3 61.3 + - + +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LYS* 2.8 23.7 + - - -
76B ILE* 5.1 1.8 - - + +
79B LEU* 4.2 21.1 - - + -
80B ARG* 4.4 11.4 - - + +
83B GLN* 3.6 13.9 - - - +
91B LEU* 3.6 22.2 - - + -
138B VAL* 3.6 14.1 - - + +
139B LEU* 3.2 16.3 + - - +
140B GLU 4.0 1.7 - - - +
141B ALA* 1.3 86.2 - - + +
143B ASN* 1.3 62.2 + - - +
144B LEU 3.7 18.6 - - - +
146B LEU* 4.3 8.1 - - + -
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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
------------------------------------------------------------
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