Contacts of the strand formed by residues 103 - 111 (chain B) in PDB entry 1IC1
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 ASN 103 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LYS* 1.3 72.6 - - - +
104B LEU* 1.3 62.9 + - - +
105B THR* 3.6 2.1 + - - +
145B THR* 2.6 21.1 + - - +
146B VAL 4.1 2.7 - - - -
147B LEU* 3.3 26.7 - - + +
311B NAG 1.5 63.1 - - - +
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Residues in contact with LEU 104 (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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94B LEU* 4.0 15.7 - - + -
98B GLN* 3.3 42.6 - - + +
102B LYS* 2.7 22.8 + - + +
103B ASN* 1.3 72.6 - - - +
105B THR* 1.3 62.0 + - - +
106B LEU* 3.8 28.2 + - + -
145B THR* 3.2 4.4 - - - +
146B VAL* 2.8 46.1 + - + +
148B VAL* 3.7 16.2 - - + -
180B TYR* 4.3 10.5 - - + +
182B LEU* 4.5 10.5 - - + -
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Residues in contact with THR 105 (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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94B LEU* 3.9 15.8 - - - +
103B ASN 3.6 1.3 + - - +
104B LEU* 1.3 77.4 - - - +
106B LEU* 1.3 62.1 + - - +
107B ARG* 4.5 13.3 + - - +
143B THR* 3.5 10.9 - - - +
144B THR 3.6 2.7 - - - -
145B THR* 3.7 0.4 - - - -
311B NAG 3.0 56.1 + - - +
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Residues in contact with LEU 106 (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 LEU* 4.9 12.1 - - + -
94B LEU* 4.3 9.9 - - + -
104B LEU* 3.8 20.8 + - + -
105B THR* 1.3 70.2 - - - +
107B ARG* 1.3 63.5 + - - +
123B LEU* 5.0 6.3 - - + -
130B LEU* 4.0 11.4 - - + -
143B THR* 2.9 25.7 - - - +
144B THR* 3.0 25.3 + - + +
146B VAL* 3.4 32.5 - - + -
157B PHE* 3.7 29.8 - - + -
180B TYR* 4.2 22.7 - - + -
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Residues in contact with ARG 107 (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 LEU* 3.4 9.5 - - - +
92B ALA* 2.8 47.8 + - + +
94B LEU* 4.9 4.0 - - + +
105B THR* 4.5 16.3 + - - +
106B LEU* 1.3 76.7 - - - +
108B CYS* 1.3 61.1 + - - +
109B GLN* 4.1 1.6 - - - +
123B LEU* 5.1 0.6 - - - +
141B GLU* 3.4 38.7 + - - +
142B VAL 3.5 6.7 - - - +
143B THR* 3.9 32.1 + - + +
311B NAG 5.6 5.1 + - - -
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Residues in contact with CYS 108 (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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90B GLU 3.9 6.7 - - - -
91B LEU* 3.7 5.9 - - + +
107B ARG* 1.3 73.8 - - - +
109B GLN* 1.3 66.7 + - - +
110B VAL* 3.5 20.2 - - - -
123B LEU* 3.5 8.3 - - + +
140B ALA 3.6 0.9 - - - +
141B GLU* 3.4 8.3 - - - +
142B VAL* 3.0 42.6 + - + +
159B CYS* 2.0 53.6 - - + -
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Residues in contact with GLN 109 (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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88B ARG* 3.4 29.4 + - + +
90B GLU 2.8 39.3 + - - +
92B ALA* 4.2 21.6 - - - +
93B PRO* 5.4 2.4 - - - +
107B ARG* 4.1 9.0 - - - +
108B CYS* 1.3 77.2 - - - +
110B VAL* 1.3 61.5 + - - +
111B GLU* 6.2 0.4 - - - +
139B PRO* 5.0 11.4 - - + +
140B ALA 3.6 4.0 - - - -
141B GLU* 3.1 28.0 + - + +
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Residues in contact with VAL 110 (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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86B PRO* 4.2 14.6 - - + -
88B ARG 3.0 2.7 - - - -
89B VAL* 3.4 30.3 - - + -
108B CYS* 3.5 22.0 - - - -
109B GLN* 1.3 80.5 - - - +
111B GLU* 1.3 65.9 + - - +
112B GLY 5.1 2.7 - - - +
116B ARG* 3.5 4.5 + - - +
119B LEU* 5.1 4.7 - - + -
121B VAL* 3.9 25.6 - - + -
139B PRO* 3.0 5.3 - - - +
140B ALA* 2.6 51.7 + - + +
142B VAL* 5.7 0.2 - - + -
159B CYS* 4.5 1.1 - - - -
161B THR* 5.0 2.2 - - - +
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Residues in contact with GLU 111 (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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86B PRO* 3.5 4.4 - - - +
87B GLU* 2.8 30.8 + - + +
88B ARG* 2.7 51.6 + - + +
109B GLN* 6.2 0.3 - - - +
110B VAL* 1.3 75.9 - - - +
112B GLY* 1.3 63.5 + - - +
138B GLU* 3.1 22.4 - - - +
139B PRO* 4.3 12.1 - - + +
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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