Contacts of the helix formed by residues 125 - 140 (chain B) in PDB entry 5C1V
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 PHE 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU 4.4 12.6 - - - -
51B MET 5.8 0.4 - - - -
53B GLU* 4.6 15.7 - - + -
93B GLY 3.2 11.3 + - - +
94B GLN* 5.1 5.2 - - - -
95B PHE* 3.4 28.0 - + + -
96B PHE* 4.2 25.1 - + - -
123B GLY 3.1 1.6 - - - -
124B TYR* 1.3 117.6 - + + +
126B SER* 1.3 61.0 + - - +
128B GLU* 3.3 38.9 + - + +
129B CYS* 3.2 23.9 + - - -
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B GLY* 3.7 13.4 - - - -
119B TYR 4.5 1.3 - - - -
120B VAL* 3.8 6.6 - - - +
121B ASP* 3.1 27.7 + - - -
123B GLY 3.2 11.6 + - - -
125B PHE* 1.3 70.8 - - - +
127B ILE* 1.3 64.8 + - - -
129B CYS* 3.4 3.1 + - - +
130B VAL* 3.1 26.5 + - - +
162B PHE* 3.6 20.1 - - - +
165B GLU* 2.8 22.4 + - - -
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B SER* 1.3 74.6 - - - +
128B GLU* 1.3 79.5 + - + +
130B VAL* 4.4 4.5 - - + -
131B LEU* 2.9 42.5 + - + +
162B PHE* 3.9 25.9 - - + -
165B GLU* 2.7 22.1 + - + +
166B CYS* 4.1 13.5 - - - -
169B LYS* 3.9 18.4 - - + -
170B TYR* 3.9 31.9 - - + -
174B VAL* 4.1 9.0 - - + -
178B CYS* 4.1 13.5 - - - -
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.8 35.9 - - + +
53B GLU* 5.0 4.3 - - - -
54B GLY 4.4 11.2 - - - +
55B ARG* 5.9 0.5 - - - +
95B PHE* 3.9 18.8 - - + -
125B PHE* 3.3 40.0 - - + +
126B SER 3.2 0.6 - - - -
127B ILE* 1.3 88.7 - - + +
129B CYS* 1.3 60.4 + - - +
131B LEU* 4.5 3.1 - - + -
132B TYR* 2.8 31.9 + - - +
169B LYS* 2.7 30.2 + - - +
170B TYR* 6.1 1.3 - - - +
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Residues in contact with CYS 129 (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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91B ILE* 3.6 25.6 - - + -
93B GLY* 3.9 3.8 - - - -
94B GLN 3.9 0.2 - - - -
95B PHE* 3.5 33.4 - - - -
98B LEU* 4.2 13.0 - - + -
119B TYR* 4.0 12.8 - - + +
125B PHE 3.2 13.1 + - - -
126B SER 3.6 7.6 - - - +
128B GLU* 1.3 75.5 - - - +
130B VAL* 1.3 67.9 + - - +
132B TYR* 4.6 0.2 - - - -
133B LEU* 2.9 34.2 + - + +
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Residues in contact with VAL 130 (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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65B ILE* 4.6 8.7 - - + -
119B TYR* 4.7 5.6 - - + -
120B VAL* 3.7 23.1 - - + -
126B SER 3.1 16.5 + - - +
127B ILE* 3.8 9.6 - - + +
128B GLU 3.3 0.2 - - - -
129B CYS* 1.3 78.5 - - - +
131B LEU* 1.3 67.0 + - - +
133B LEU* 4.8 1.1 - - - -
134B TRP* 2.9 59.0 + - + +
162B PHE* 4.5 6.3 - - + -
178B CYS* 4.1 19.7 - - - -
182B PHE* 3.9 17.9 - - + -
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Residues in contact with LEU 131 (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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46B LEU* 5.0 2.9 - - + +
50B LEU* 4.6 10.5 - - + -
56B LEU* 3.9 18.8 - - + -
61B ALA* 3.9 33.0 - - + +
64B ILE* 3.8 19.2 - - + +
65B ILE* 4.1 18.8 - - + -
127B ILE* 2.9 28.6 + - + +
128B GLU* 3.9 7.4 - - + +
129B CYS 3.1 0.2 - - - -
130B VAL* 1.3 77.5 - - + +
132B TYR* 1.3 63.7 + - - +
135B ALA* 3.0 23.9 + - - +
170B TYR* 3.6 34.5 - - + +
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Residues in contact with TYR 132 (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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43B VAL* 3.7 24.9 + - + +
44B ASP* 5.6 0.3 - - - -
46B LEU* 3.7 20.2 - - + -
47B LYS* 3.6 40.1 - - + +
50B LEU* 4.6 1.9 - - + +
95B PHE* 3.9 15.7 - + + -
98B LEU* 4.5 3.8 - - + -
99B MET* 3.7 24.2 - - + -
102B PHE* 3.9 15.7 - + - -
108B PRO* 5.9 1.0 - - - +
128B GLU 2.8 17.8 + - - +
129B CYS* 3.9 2.9 - - - +
131B LEU* 1.3 78.0 - - - +
133B LEU* 1.3 63.0 + - - +
135B ALA* 3.2 7.8 + - + +
136B LEU* 3.1 53.6 + - + +
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Residues in contact with LEU 133 (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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91B ILE* 5.0 6.3 - - + -
98B LEU* 3.9 23.3 - - + -
102B PHE* 4.4 9.6 - - + -
115B PHE* 4.0 33.2 - - + -
119B TYR* 4.0 32.8 - - + -
129B CYS* 2.9 25.1 + - + +
130B VAL 4.0 1.1 - - - +
132B TYR* 1.3 74.8 - - - +
134B TRP* 1.3 68.5 + - + +
136B LEU* 3.1 7.2 + - + +
137B LYS* 2.9 27.4 + - - +
144B LEU* 4.3 7.9 - - + +
146B LEU* 4.1 18.0 - - + +
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Residues in contact with TRP 134 (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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64B ILE* 3.7 19.1 - - + -
65B ILE* 3.7 21.0 + - + +
68B GLY* 3.6 24.7 - - - -
69B ALA 3.9 2.0 - - - +
72B LEU* 3.8 29.8 - - + +
119B TYR* 4.2 17.0 - + - -
130B VAL* 2.9 52.3 + - + +
131B LEU* 4.7 0.2 - - - -
133B LEU* 1.3 81.7 - - + +
135B ALA* 1.3 62.5 + - - +
137B LYS* 3.3 8.1 + - + +
138B ILE* 3.1 27.4 + - - +
146B LEU* 4.3 12.8 - - + -
181B ALA* 4.0 12.8 - - + +
182B PHE* 3.4 35.7 - + - -
185B LEU* 4.1 19.1 - - + -
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Residues in contact with ALA 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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41B PRO* 3.5 23.6 - - + +
43B VAL* 4.4 14.1 - - + -
46B LEU* 4.8 10.8 - - + -
64B ILE* 4.0 12.5 - - + +
131B LEU 3.0 19.5 + - - +
132B TYR* 3.3 8.7 - - + +
134B TRP* 1.3 79.1 - - - +
136B LEU* 1.3 62.7 + - - +
138B ILE* 3.5 11.4 + - - +
139B LEU* 3.1 17.0 + - - +
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Residues in contact with LEU 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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43B VAL* 3.4 37.0 - - + -
102B PHE* 3.7 17.0 - - + -
108B PRO* 3.7 28.3 - - + -
132B TYR* 3.1 42.7 + - + +
133B LEU* 3.1 9.1 + - - +
135B ALA* 1.3 77.5 - - - +
137B LYS* 1.3 53.3 - - - +
139B LEU* 4.3 2.5 - - - -
140B TYR* 2.8 48.1 + - + +
144B LEU* 4.0 15.3 - - + +
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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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68B GLY* 4.8 5.2 - - - +
71B ILE* 3.9 18.0 - - + +
72B LEU* 3.8 17.7 - - + +
75B GLU* 3.1 39.8 + - - -
133B LEU 2.9 13.2 + - - +
134B TRP* 3.4 15.0 - - + +
135B ALA 3.2 0.2 - - - -
136B LEU* 1.3 75.3 - - - +
138B ILE* 1.3 65.1 + - + +
140B TYR 4.6 0.4 - - - -
141B PRO* 3.0 38.4 - - + +
144B LEU* 3.2 32.0 + - + +
145B PHE* 3.6 14.5 - - - +
146B LEU* 3.6 22.3 - - + +
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Residues in contact with ILE 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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35B PHE* 4.9 6.3 - - + -
39B GLY 4.7 3.8 - - - +
40B LYS* 5.1 2.1 - - + +
41B PRO* 3.7 22.4 - - + -
64B ILE* 3.6 35.4 - - + +
67B GLU* 4.1 24.9 - - + +
68B GLY* 3.9 19.5 - - - +
71B ILE* 3.6 16.5 - - + +
134B TRP 3.1 15.4 + - - +
135B ALA* 3.5 13.7 - - - +
137B LYS* 1.3 79.6 - - - +
139B LEU* 1.3 62.2 + - - +
141B PRO* 3.7 9.7 - - - +
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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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40B LYS* 3.6 40.6 - - + -
41B PRO* 3.8 15.9 - - + +
43B VAL* 3.8 28.7 - - + -
135B ALA 3.1 14.4 + - - +
136B LEU 3.8 4.0 - - - +
137B LYS 3.2 0.2 - - - -
138B ILE* 1.3 83.0 - - - +
140B TYR* 1.3 97.9 + - + +
141B PRO* 3.4 6.8 - - - +
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Residues in contact with TYR 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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43B VAL* 5.1 4.9 - - + +
107B SER* 5.2 0.9 + - - -
108B PRO* 3.8 34.7 - - + +
109B ALA* 3.3 38.0 + - + +
136B LEU* 2.8 31.5 + - + +
137B LYS* 3.5 3.2 - - - +
139B LEU* 1.3 108.8 - - + +
141B PRO* 1.3 63.8 - - - +
142B LYS 3.0 6.4 + - - -
143B THR* 3.3 27.8 - - + +
144B LEU* 3.0 24.6 + - + +
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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
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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