Contacts of the helix formed by residues 134 - 149 (chain G) in PDB entry 1IB1
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 GLY 134 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D LYS* 6.2 1.6 - - - -
132G GLN 3.5 0.4 - - - -
133G GLN* 1.3 72.9 - - - +
135G LYS* 1.3 59.4 + - - +
137G SER* 3.3 6.7 + - - -
138G VAL* 3.1 28.9 + - - +
402G COT 2.5 37.6 + - - -
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Residues in contact with LYS 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LYS* 4.0 13.5 - - - +
14C GLU* 5.0 3.2 + - - -
39C GLU* 3.8 11.9 + - - +
42C ASN* 5.5 2.4 + - - -
43C LEU* 4.2 18.4 - - - +
35G ASN* 5.8 0.2 - - - +
84G TRP* 3.7 51.2 - - + -
91G VAL* 6.2 2.9 - - + -
92G ALA* 5.3 5.0 - - + +
126G VAL* 4.8 7.4 - - + -
130G PHE* 3.7 18.2 - - + +
133G GLN* 3.3 51.6 - - + +
134G GLY* 1.3 76.7 - - - +
136G GLY* 1.3 64.6 + - - +
138G VAL* 5.8 0.2 - - + -
139G LEU* 3.1 24.4 + - - +
402G COT 3.8 1.9 + - - +
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Residues in contact with GLY 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G LEU* 4.6 6.0 - - - +
126G VAL* 3.6 14.8 - - - +
135G LYS* 1.3 74.4 - - - +
137G SER* 1.3 55.4 - - - +
139G LEU* 3.6 7.1 + - - +
140G LEU* 3.0 28.6 + - - +
167G PHE* 4.9 5.9 - - - -
402G COT 2.7 37.1 + - - -
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Residues in contact with SER 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G GLY* 3.6 6.1 - - - -
135G LYS 3.2 0.2 - - - -
136G GLY* 1.3 75.2 - - - +
138G VAL* 1.3 58.9 + - - +
140G LEU 3.3 0.2 + - - -
141G TRP* 2.9 40.2 + - - +
167G PHE* 3.6 5.5 - - - -
170G ARG* 5.1 2.3 + - - -
171G PHE* 3.5 32.2 - - - -
402G COT 2.5 32.7 + - - -
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Residues in contact with VAL 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLN* 3.8 34.8 - - + +
37G PHE* 3.5 14.6 - - + -
84G TRP* 3.4 34.8 - - + -
134G GLY* 3.1 18.6 + - - +
135G LYS* 3.4 0.6 + - + +
137G SER* 1.3 76.5 - - - +
139G LEU* 1.3 56.6 + - - +
141G TRP* 3.6 6.3 + - - +
142G ARG* 2.9 39.1 + - - +
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Residues in contact with LEU 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G PHE* 3.8 20.6 - - + -
82G LEU* 3.8 38.8 - - + +
83G GLY* 4.5 0.9 - - - -
84G TRP* 4.5 11.9 - - + +
92G ALA* 3.9 8.1 - - + -
93G PHE 3.6 39.9 - - - +
94G ILE* 3.7 15.3 - - + -
124G LEU* 3.9 10.5 - - + -
135G LYS 3.1 17.5 + - - +
136G GLY* 3.6 4.5 - - - +
138G VAL* 1.3 74.0 - - - +
140G LEU* 1.3 59.8 + - - +
142G ARG* 3.1 3.5 + - - +
143G TYR* 2.8 26.9 + - - +
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Residues in contact with LEU 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G ILE* 3.9 15.0 - - + +
121G LEU* 3.7 30.1 - - + -
124G LEU* 4.3 9.6 - - + -
136G GLY 3.0 18.9 + - - +
137G SER 3.9 2.9 - - - +
139G LEU* 1.3 74.5 - - - +
141G TRP* 1.3 64.4 + - - +
143G TYR* 3.2 3.0 + - + +
144G LEU* 3.0 35.8 + - + +
167G PHE* 4.6 2.2 - - + -
168G TYR* 3.7 26.0 - - + -
171G PHE* 3.5 43.5 - - + -
173G PHE* 4.4 11.0 - - + -
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Residues in contact with TRP 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D LYS* 3.9 37.8 - - + +
137G SER* 2.9 27.1 + - - +
138G VAL* 3.8 5.8 - - - +
140G LEU* 1.3 75.0 - - - +
142G ARG* 1.3 64.6 + - - +
144G LEU* 3.0 22.8 + - + +
145G HIS* 3.2 30.2 + - + -
170G ARG 3.5 20.7 + - - -
171G PHE* 3.7 43.8 - + - -
22H GLY* 4.3 12.6 - - - -
24H PRO* 3.7 28.9 - - + -
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Residues in contact with ARG 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLN* 6.3 0.8 - - - +
37G PHE* 3.2 55.7 - - + +
82G LEU* 3.9 10.1 - - + -
138G VAL* 2.9 25.1 + - - +
139G LEU* 3.2 9.4 - - - +
141G TRP* 1.3 76.4 - - - +
143G TYR* 1.3 56.6 + - - +
145G HIS* 3.1 10.1 + - - +
146G HIS* 2.9 28.2 + - + +
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Residues in contact with TYR 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G LEU* 2.8 39.6 + - - +
81G SER* 4.1 4.7 - - - -
82G LEU* 3.8 27.3 - - + +
94G ILE* 3.5 35.2 - - + -
96G GLY* 3.6 12.8 - - - -
97G SER 4.6 0.2 + - - -
119G ALA* 4.3 8.3 - - + +
120G HIS 4.5 1.0 + - - -
121G LEU* 3.6 35.6 - - + +
139G LEU 2.8 18.7 + - - +
140G LEU 3.2 4.7 + - - +
142G ARG* 1.3 74.6 - - - +
144G LEU* 1.3 62.0 + - + +
146G HIS* 3.6 3.9 - + - +
147G VAL* 3.0 62.1 + - + +
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Residues in contact with LEU 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G LEU* 5.3 0.7 - - + -
140G LEU* 3.0 27.3 + - + +
141G TRP* 3.0 19.9 + - + +
143G TYR* 1.3 85.0 - - + +
145G HIS* 1.3 56.0 + - - +
147G VAL* 4.1 3.8 - - + -
148G GLY* 3.0 25.1 + - - -
156G ALA* 3.9 27.8 - - + -
171G PHE* 3.8 37.0 - - + +
173G PHE* 4.0 17.5 - - + -
193G CYS* 4.5 5.2 - - - -
195G LEU* 3.7 10.3 - - + +
24H PRO* 3.3 23.4 - - + +
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Residues in contact with HIS 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G TRP* 3.2 37.6 + + + +
142G ARG* 3.1 10.6 + - - +
144G LEU* 1.3 77.0 - - - +
146G HIS* 1.3 63.8 + - - +
148G GLY* 3.9 0.3 - - - -
149G ALA* 3.1 25.3 + - - +
19H GLY* 5.8 2.9 - - - -
20H ILE 3.6 27.9 + - - -
21H PRO* 4.5 3.2 - - + +
22H GLY 4.1 10.9 + - - -
23H SER 4.0 1.1 + - - -
24H PRO* 3.4 42.4 + - + +
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Residues in contact with HIS 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G CYS* 3.8 23.8 - - - -
79G GLU* 2.9 30.1 + - + -
81G SER 4.3 9.6 - - - -
82G LEU* 4.6 15.7 - - + +
142G ARG* 2.9 16.5 + - + +
143G TYR* 3.6 12.8 - + - +
145G HIS* 1.3 80.3 - - - +
147G VAL* 1.3 68.0 + - + +
149G ALA* 3.6 13.2 - - - +
150G GLN* 3.4 20.4 + - - +
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Residues in contact with VAL 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G GLU 4.5 1.1 - - - +
80G LEU* 4.1 18.4 - - + -
119G ALA* 3.9 23.1 - - + -
143G TYR* 3.0 59.1 + - + +
144G LEU* 3.9 8.7 - - + +
146G HIS* 1.3 86.7 - - + +
148G GLY* 1.3 69.5 + - - +
149G ALA 3.1 2.5 - - - -
150G GLN* 3.0 28.6 + - - +
153G VAL* 3.4 14.2 - - + +
156G ALA* 5.7 0.4 - - + -
195G LEU* 4.4 8.1 - - + -
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Residues in contact with GLY 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G LEU 3.0 23.4 + - - -
145G HIS 3.9 0.7 - - - -
146G HIS 3.4 0.2 - - - -
147G VAL* 1.3 77.8 - - - +
149G ALA* 1.3 59.7 + - - +
150G GLN 3.4 0.7 + - - +
153G VAL 4.4 0.7 - - - -
195G LEU* 3.9 17.7 - - - -
196G ARG* 3.3 27.9 - - - +
24H PRO 4.2 5.4 - - - -
25H GLY* 3.8 16.3 - - - +
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Residues in contact with ALA 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G HIS 3.1 17.7 + - - +
146G HIS* 3.6 9.0 - - - +
148G GLY* 1.3 76.1 - - - +
150G GLN* 1.3 63.4 + - + +
151G PRO* 3.2 10.4 - - - +
196G ARG* 5.4 0.8 - - - -
24H PRO 4.4 2.7 + - - +
25H GLY* 5.5 1.1 - - - -
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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
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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