Contacts of the strand formed by residues 118 - 126 (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 SER 118 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98G LEU* 3.4 8.3 - - - -
99G TRP* 3.0 35.8 + - - -
101G GLU 5.1 0.2 - - - -
116G GLY 3.8 0.4 - - - -
117G HIS* 1.3 102.7 + - - +
119G ALA* 1.3 59.9 + - - +
120G HIS 3.2 3.5 + - - -
155G ARG* 3.3 41.3 + - - +
157G VAL* 4.3 13.0 - - - -
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Residues in contact with ALA 119 (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* 4.7 4.3 - - + -
97G SER 3.8 4.5 - - - -
98G LEU* 4.3 3.6 - - - -
118G SER* 1.3 68.7 - - - +
120G HIS* 1.3 60.4 + - - +
121G LEU* 3.3 9.0 - - - +
143G TYR* 4.3 14.8 - - + +
147G VAL* 3.9 24.7 - - + -
153G VAL* 3.6 21.3 - - + +
155G ARG 2.9 11.2 + - - +
156G ALA* 3.3 4.4 - - + -
157G VAL* 2.9 23.9 + - - -
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Residues in contact with HIS 120 (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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96G GLY* 3.1 24.2 - - - -
97G SER* 2.8 20.1 + - - +
99G TRP* 4.2 14.3 - - + +
104G LEU* 3.5 42.8 - - + +
108G SER* 3.5 22.2 + - - -
109G LEU* 4.4 8.3 - - + -
111G LEU 5.1 0.6 + - - -
118G SER 3.2 2.0 + - - -
119G ALA* 1.3 70.5 - - - +
121G LEU* 1.3 70.4 + - - +
122G HIS* 3.1 39.9 + + - +
143G TYR* 5.0 0.4 - - - -
157G VAL* 3.4 18.2 - - + -
158G LEU* 4.8 0.6 - - - -
159G MET* 4.6 9.9 - - - +
181G ILE* 4.7 0.7 - - + -
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Residues in contact with LEU 121 (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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94G ILE* 4.0 20.0 - - + -
95G ILE 3.8 5.2 - - - -
96G GLY* 4.5 1.8 - - - -
119G ALA 3.3 16.8 - - - +
120G HIS* 1.3 75.2 + - - +
122G HIS* 1.3 64.4 + - - +
123G ALA* 3.4 4.8 - - - +
124G LEU* 5.3 6.3 - - + -
140G LEU* 3.7 31.0 - - + -
143G TYR* 3.6 28.7 - - + -
144G LEU* 5.3 0.2 - - + -
156G ALA* 4.2 15.0 - - + -
157G VAL 2.8 19.0 + - - +
158G LEU* 3.8 33.0 - - + +
159G MET* 4.8 2.8 + - - +
173G PHE* 4.6 3.6 - - + -
402G COT 4.9 6.1 + - + -
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Residues in contact with HIS 122 (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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64G PRO* 3.5 6.8 - - - +
65G LEU* 4.0 21.6 - - + +
73G PHE* 3.4 16.5 - + - -
95G ILE 2.9 9.6 + - - +
96G GLY* 3.6 15.5 - - - -
97G SER* 2.6 28.4 + - - -
108G SER 3.5 5.8 - - - -
109G LEU* 3.3 34.5 + - + +
120G HIS* 3.1 56.8 + + - -
121G LEU* 1.3 73.9 - - - +
123G ALA* 1.3 61.4 + - - +
159G MET* 5.3 4.9 - - - +
402G COT 3.2 22.6 - - - -
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Residues in contact with ALA 123 (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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52G GLU* 4.7 3.1 - - - +
56G PHE* 4.9 1.8 - - + -
64G PRO* 3.5 24.2 - - + -
65G LEU* 4.5 12.3 - - + -
93G PHE* 3.9 21.7 - - + -
94G ILE* 3.2 7.6 - - - +
95G ILE* 3.0 27.2 + - + +
121G LEU* 3.4 2.8 - - - -
122G HIS* 1.3 80.8 - - - +
124G LEU* 1.3 61.1 + - - +
402G COT 3.3 8.1 - - - -
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Residues in contact with LEU 124 (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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56G PHE* 3.6 3.7 - - - -
93G PHE 3.5 17.0 - - - +
94G ILE* 3.5 19.1 - - + -
121G LEU* 5.3 6.7 - - + -
123G ALA* 1.3 75.9 - - - +
125G ALA* 1.3 67.1 + - - +
126G VAL* 5.3 0.2 - - + -
136G GLY* 4.6 10.3 - - - +
139G LEU* 3.9 11.4 - - + -
140G LEU* 4.3 20.0 - - + -
158G LEU* 5.6 0.4 - - + -
167G PHE* 4.8 3.1 - - + -
168G TYR* 3.2 38.8 - - + +
402G COT 2.9 56.6 + - + +
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Residues in contact with ALA 125 (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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51G ILE* 3.8 11.9 - - + -
55G ALA* 4.5 1.6 - - + -
56G PHE* 3.7 18.4 - - + -
92G ALA* 3.3 4.0 - - - +
93G PHE* 3.0 59.0 + - + +
124G LEU* 1.3 77.7 - - - +
126G VAL* 1.3 65.9 + - - +
402G COT 3.4 13.9 - - + +
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Residues in contact with VAL 126 (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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51G ILE* 4.3 4.5 - - - +
91G VAL* 3.7 9.2 - - + +
92G ALA* 4.0 11.7 - - + -
124G LEU* 5.3 2.2 - - + -
125G ALA* 1.3 78.5 - - - +
127G HIS* 1.3 76.6 + - - +
130G PHE* 3.8 26.9 - - + +
131G ARG* 2.9 33.0 + - + +
135G LYS* 5.0 4.5 - - + -
136G GLY* 3.6 15.9 - - - -
402G COT 2.6 48.5 + - + +
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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