Contacts of the helix formed by residues 113 - 128 (chain B) in PDB entry 4RG7
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 SER 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A HIS* 2.7 36.2 + - - -
69B PRO* 5.9 2.9 - - - -
70B GLN* 5.7 3.7 + - - -
73B TYR* 4.6 10.4 - - - -
110B PHE* 2.7 26.5 + - - -
112B ASP* 1.3 71.8 - - - +
114B ALA* 1.3 62.0 + - - +
115B CYS 3.4 0.9 - - - -
116B PHE* 3.4 8.6 + - - +
117B THR* 3.1 24.9 + - - +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B VAL* 3.8 32.5 - - + +
110B PHE* 3.5 4.5 + - + -
111B GLY 3.1 20.3 + - - +
112B ASP 3.0 1.6 - - - -
113B SER* 1.3 78.4 - - - +
115B CYS* 1.3 63.9 + - - +
117B THR* 3.0 24.7 - - + +
118B LEU* 3.1 22.6 + - + +
144B LEU* 5.5 5.8 - - + -
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Residues in contact with CYS 115 (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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112B ASP 3.6 11.8 + - - -
114B ALA* 1.3 78.0 - - - +
116B PHE* 1.3 83.7 + - - +
118B LEU* 4.7 0.4 - - - -
119B SER* 3.0 27.0 + - - -
141B SER* 3.4 27.2 - - - +
144B LEU* 4.1 10.4 - - + +
145B ASN* 3.5 43.5 - - + -
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Residues in contact with PHE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA 5.2 1.1 - - - -
14A GLN* 4.1 8.5 - - + -
15A ALA* 3.7 37.7 - - + -
18A HIS* 3.5 34.1 - + + -
20A ALA* 3.7 24.0 - - + -
23A ASP* 5.5 3.1 - - + -
73B TYR* 3.4 25.5 + - + +
112B ASP 4.3 3.6 - - - -
113B SER* 3.9 8.5 - - - +
114B ALA 3.3 0.6 - - - -
115B CYS* 1.3 97.7 - - - +
117B THR* 1.3 61.0 + - - +
118B LEU 3.2 0.4 - - - -
119B SER* 3.3 8.2 + - - -
120B LEU* 2.9 29.1 + - - +
145B ASN* 4.3 11.7 - - - -
148B LEU* 5.8 5.2 - - + -
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Residues in contact with THR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR* 3.7 18.9 - - - -
92B LEU* 3.5 24.9 - - - +
106B ILE* 3.9 9.8 - - + +
110B PHE* 3.6 29.9 - - + -
113B SER 3.1 16.5 + - - +
114B ALA* 3.0 26.0 - - - +
116B PHE* 1.3 74.8 - - - +
118B LEU* 1.3 58.4 + - - +
120B LEU* 3.3 6.5 + - - +
121B LEU* 2.9 29.7 + - - +
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B HIS* 4.9 14.8 - - + +
106B ILE* 3.7 39.3 - - + -
107B VAL* 5.6 4.3 - - + -
114B ALA* 3.1 31.7 + - + +
115B CYS* 4.0 3.6 - - - +
117B THR* 1.3 74.5 - - - +
119B SER* 1.3 67.7 + - - +
121B LEU* 3.2 6.8 + - + +
122B GLY* 2.9 19.9 + - - -
137B CYS* 3.6 37.7 - - - +
140B LYS* 4.0 25.6 - - + +
141B SER* 4.2 7.4 - - - +
144B LEU* 5.6 2.9 - - + -
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B CYS 3.0 20.9 + - - -
116B PHE* 3.4 11.2 - - - -
118B LEU* 1.3 76.2 - - - +
120B LEU* 1.3 60.6 + - - +
123B HIS* 3.1 20.6 + - - +
138B TYR* 3.1 24.6 - - - -
141B SER* 4.0 8.6 - - - -
150B SER* 4.2 8.8 + - - -
151B PRO* 4.0 18.0 - - - +
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Residues in contact with LEU 120 (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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73B TYR* 5.1 11.7 - - + +
76B ALA* 4.1 15.7 - - + +
77B LYS* 3.9 34.3 - - + +
80B VAL* 4.0 21.5 - - + -
88B GLY* 6.4 0.2 - - - -
116B PHE 2.9 16.5 + - - +
117B THR* 3.6 7.4 - - - +
118B LEU 3.2 0.2 - - - -
119B SER* 1.3 73.1 - - - +
121B LEU* 1.3 65.2 + - - +
123B HIS* 3.3 18.0 - - + +
124B VAL* 3.0 27.3 + - + +
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLY 4.8 1.6 - - - +
89B GLU* 4.2 26.0 - - + -
92B LEU* 4.0 13.9 - - + -
93B SER* 3.9 20.0 - - - +
106B ILE* 3.7 30.1 - - + -
117B THR* 2.9 15.4 + - - +
118B LEU* 3.5 10.8 - - + +
120B LEU* 1.3 74.5 - - - +
122B GLY* 1.3 56.2 + - - +
124B VAL* 2.9 11.2 + - + +
125B TYR* 2.7 57.0 + - + +
137B CYS* 4.0 17.0 - - - -
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Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU 2.9 14.0 + - - -
119B SER 3.3 4.5 + - - -
121B LEU* 1.3 74.4 - - - +
123B HIS* 1.3 51.6 + - - +
125B TYR* 3.3 1.4 + - - +
126B CYS* 2.8 39.5 + - - -
134B GLY* 3.6 27.8 - - - -
137B CYS* 3.8 4.3 - - - +
138B TYR* 3.3 12.6 - - - -
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Residues in contact with HIS 123 (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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80B VAL* 5.3 6.5 - - + -
119B SER 3.1 9.2 + - - +
120B LEU* 3.3 27.4 - - + +
122B GLY* 1.3 75.7 - - - +
124B VAL* 1.3 56.7 + - + +
126B CYS* 3.2 5.1 + - - +
127B LYS* 2.8 43.2 + - + +
138B TYR* 3.0 20.0 + - - +
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 5.1 8.7 - - + -
85B LEU* 3.7 38.1 - - + +
88B GLY* 5.1 4.0 - - - -
89B GLU* 4.2 20.6 - - + +
120B LEU* 3.0 28.4 + - + +
121B LEU* 2.9 17.1 + - + +
123B HIS* 1.3 74.1 - - + +
125B TYR* 1.3 65.8 + - + +
127B LYS* 3.1 7.2 + - - +
128B THR* 2.8 36.3 + - + +
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Residues in contact with TYR 125 (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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89B GLU* 5.4 9.0 - - + -
93B SER* 3.9 13.9 + - - -
100B GLN* 3.7 22.2 + - - -
103B HIS* 6.1 0.9 - + - -
121B LEU* 2.7 37.1 + - + +
124B VAL* 1.3 75.3 - - + +
126B CYS* 1.3 56.9 + - - +
128B THR* 2.9 32.1 + - - +
130B ARG* 3.0 34.5 + - + +
133B LYS* 3.5 33.7 - - + -
134B GLY* 3.5 11.2 - - - -
137B CYS* 3.6 25.4 - - - -
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Residues in contact with CYS 126 (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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122B GLY 2.8 24.0 + - - +
123B HIS* 3.6 8.5 - - - +
125B TYR* 1.3 75.7 - - - +
127B LYS* 1.3 59.4 + - - +
128B THR 3.0 8.8 - - - +
130B ARG 4.6 1.1 - - - -
131B LEU* 4.7 14.1 - - - +
134B GLY* 4.3 11.4 - - - -
135B SER* 4.9 0.9 - - - -
138B TYR* 3.5 27.1 - - - +
154B SER* 5.8 0.2 - - - -
158B ILE* 5.3 12.8 - - - -
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Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 5.7 6.5 - - + -
123B HIS* 2.8 28.5 + - + +
124B VAL* 3.5 7.6 - - + +
126B CYS* 1.3 75.7 - - - +
128B THR* 1.3 66.3 + - + +
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Residues in contact with THR 128 (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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85B LEU* 4.9 12.3 - - + -
124B VAL* 2.8 27.1 + - + +
125B TYR* 2.9 29.6 + - - +
126B CYS* 3.0 8.8 - - - +
127B LYS* 1.3 82.8 - - + +
129B ASP* 1.3 61.4 + - - +
130B ARG* 3.2 8.2 + - - +
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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