Contacts of the helix formed by residues 123 - 137 (chain F) in PDB entry 4G7H
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 ASP 123 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121F GLY 4.3 0.4 + - - -
122F LEU* 1.3 71.7 - - - +
124F PRO* 1.3 71.0 - - - +
125F ASP* 2.9 28.3 - - - +
126F LEU* 3.4 22.0 + - + +
127F ILE* 3.0 25.2 + - - +
147F LEU* 5.4 6.4 - - - +
148F LYS* 5.4 13.6 + - - +
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Residues in contact with PRO 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ILE* 3.5 19.3 - - + +
114F LYS* 5.5 13.2 - - + +
117F SER* 3.3 29.4 - - - +
122F LEU 3.2 5.8 - - - +
123F ASP* 1.3 87.4 - - + +
125F ASP* 1.3 66.3 + - - +
127F ILE* 3.5 2.8 + - + -
128F ARG* 2.9 31.0 + - - +
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Residues in contact with ASP 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F ASP* 2.9 23.7 - - - +
124F PRO* 1.3 82.6 - - - +
126F LEU* 1.3 59.8 + - - +
128F ARG* 3.2 30.9 + - - +
129F GLU* 2.9 35.8 + - - +
147F LEU* 3.9 17.5 - - + -
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Residues in contact with LEU 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F LEU* 4.5 16.2 - - + -
123F ASP* 3.1 24.1 + - + +
125F ASP* 1.3 78.4 - - - +
127F ILE* 1.3 56.9 + - - +
129F GLU* 3.3 1.7 + - - +
130F VAL* 2.9 41.9 + - + +
147F LEU* 4.5 15.6 - - + +
149F GLU* 3.8 34.1 - - + +
151F LEU* 3.9 24.7 - - + -
155F THR* 4.9 3.1 - - + -
159F ILE* 4.1 28.3 - - + -
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Residues in contact with ILE 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F ILE* 4.2 13.9 - - + +
116F LEU* 3.6 30.5 - - + +
117F SER* 3.5 36.8 - - - +
120F THR* 4.7 2.5 - - - +
122F LEU* 4.0 24.5 - - + -
123F ASP 3.0 18.7 + - - +
124F PRO* 3.6 6.5 - - + +
126F LEU* 1.3 75.8 - - - +
128F ARG* 1.3 57.7 + - - +
130F VAL* 3.2 6.9 + - - +
131F VAL* 2.9 48.3 + - + +
159F ILE* 5.1 3.4 - - + -
163F LEU* 4.4 12.3 - - + -
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Residues in contact with ARG 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ILE* 3.8 31.6 - - + +
124F PRO 2.9 20.5 + - - +
125F ASP* 3.2 35.1 + - - +
127F ILE* 1.3 75.1 - - - +
129F GLU* 1.3 84.7 + - - +
131F VAL* 3.8 2.3 - - - +
132F ARG* 2.9 53.8 + - - +
144F ILE* 5.4 3.6 - - - +
147F LEU* 5.1 2.8 - - - +
181F GLU* 3.8 12.6 - - - +
225F GLU* 6.0 1.6 - - - -
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Residues in contact with GLU 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559D ALA 4.4 2.4 - - - +
125F ASP 2.9 19.2 + - - +
126F LEU 3.8 4.0 - - - +
127F ILE 3.2 0.2 - - - -
128F ARG* 1.3 111.3 + - - +
130F VAL* 1.3 58.9 + - - +
132F ARG* 3.8 24.5 + - - +
133F ALA* 2.9 30.4 + - - +
144F ILE* 3.8 26.9 - - + +
147F LEU* 3.8 25.8 - - + -
151F LEU* 3.7 22.9 - - + +
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Residues in contact with VAL 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F LEU* 2.9 32.6 + - + +
127F ILE* 3.7 4.3 - - - +
129F GLU* 1.3 74.4 - - - +
131F VAL* 1.3 66.1 + - + +
133F ALA* 3.1 8.1 + - - +
134F LYS* 2.9 23.6 + - + +
151F LEU* 4.6 2.9 - - + -
155F THR 5.3 0.2 - - - -
156F VAL* 3.8 37.9 - - + +
159F ILE* 3.7 29.8 - - + -
160F ASP* 3.9 24.0 - - + +
163F LEU* 4.9 4.7 - - + -
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Residues in contact with VAL 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ILE* 5.0 1.3 - - + -
127F ILE* 2.9 35.7 + - + +
128F ARG* 3.8 5.8 - - - +
130F VAL* 1.3 76.7 - - - +
132F ARG* 1.3 58.4 + - - +
134F LYS* 3.1 5.8 + - - +
135F ILE* 3.0 26.7 + - - +
160F ASP* 5.8 0.7 - - - -
163F LEU* 4.7 3.6 - - + -
174F LEU* 4.4 18.2 - - + -
177F ALA* 3.7 21.5 - - + +
178F ARG* 3.6 45.6 - - - +
181F GLU* 3.8 10.1 - - + -
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Residues in contact with ARG 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559D ALA 4.2 4.0 + - - -
560D GLN* 3.5 21.6 + - - +
561D GLY* 4.0 18.6 - - - +
128F ARG* 2.9 40.3 + - - +
129F GLU* 3.8 28.9 + - - +
131F VAL* 1.3 73.7 - - - +
133F ALA* 1.3 60.4 + - - +
135F ILE* 3.2 1.5 + - + +
136F LEU* 2.9 47.1 + - + +
181F GLU* 2.8 45.3 + - + +
184F ARG* 3.5 30.1 - - - +
185F GLN* 4.9 2.5 - - - +
225F GLU* 4.2 5.9 + - - -
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Residues in contact with ALA 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F GLU 2.9 19.7 + - - +
130F VAL* 3.1 9.6 + - - +
132F ARG* 1.3 74.9 - - - +
134F LYS* 1.3 58.8 + - - +
136F LEU* 4.9 2.0 - - - -
137F GLY* 3.0 35.9 + - - +
140F ARG 4.7 8.5 - - - +
141F VAL* 4.6 14.1 - - + -
151F LEU* 5.4 3.6 - - + -
156F VAL* 4.3 22.9 - - + -
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Residues in contact with LYS 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412D GLY 3.7 17.3 - - - +
413D ASP* 3.8 20.2 + - - +
414D ARG 6.0 0.4 - - - +
434D ARG* 4.4 0.2 + - - -
130F VAL* 2.9 15.4 + - + +
131F VAL 3.6 5.2 - - - +
133F ALA* 1.3 80.8 - - + +
135F ILE* 1.3 61.5 + - - +
137F GLY* 3.8 7.4 + - - -
156F VAL* 5.1 8.7 - - + +
157F GLU* 3.2 30.1 + - - -
160F ASP* 3.3 27.0 + - + +
164F LYS* 5.2 1.0 - - - +
178F ARG* 3.5 32.8 - - - +
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Residues in contact with ILE 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D TYR* 5.8 0.5 - - - -
411D THR* 3.6 25.1 - - - +
412D GLY* 4.0 9.4 - - - -
434D ARG* 2.4 37.5 + - - +
131F VAL 3.0 16.0 + - - +
132F ARG* 3.2 6.5 + - + +
134F LYS* 1.3 78.8 - - - +
136F LEU* 1.3 72.6 + - + +
137F GLY 3.5 0.5 + - - -
178F ARG* 3.5 32.5 - - - +
181F GLU* 4.0 13.9 - - + -
182F ALA* 4.0 28.5 - - + +
185F GLN* 4.6 5.4 - - + -
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Residues in contact with LEU 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D ARG* 4.9 3.5 + - - -
163D TYR* 4.5 11.6 + - - -
434D ARG* 5.1 0.2 - - - -
561D GLY* 4.5 2.9 - - - -
562D ALA 5.2 0.2 - - - +
563D PRO* 5.7 0.4 - - + -
564D GLU* 6.5 1.1 - - + -
132F ARG* 2.9 42.4 + - + +
133F ALA* 4.2 3.1 - - - +
135F ILE* 1.3 79.7 - - + +
137F GLY* 1.3 61.5 + - - +
139F ALA* 4.7 9.4 - - - +
140F ARG* 3.6 51.6 - - + +
185F GLN* 3.6 36.6 - - + +
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Residues in contact with GLY 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D ARG* 4.5 10.8 - - - -
414D ARG* 6.1 0.7 - - - -
434D ARG* 5.8 0.4 - - - -
133F ALA 3.0 18.7 + - - +
134F LYS* 3.8 6.5 + - - -
135F ILE 3.3 3.4 - - - -
136F LEU* 1.3 80.5 - - - +
138F SER* 1.3 62.3 + - - -
139F ALA 3.1 6.9 + - - -
140F ARG 3.7 12.8 + - - +
141F VAL* 4.9 2.3 - - - +
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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
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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