Contacts of the strand formed by residues 155 - 163 (chain B) in PDB entry 1IAO
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 PHE 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ASP* 4.8 3.1 - - - -
121B ASP 2.9 24.4 + - - -
122B PHE* 2.8 40.4 + - + -
123B TYR* 4.3 17.0 - + - -
124B PRO 4.2 1.8 - - - -
125B ALA* 3.4 42.8 - - + -
147B LEU* 3.9 19.5 - - + -
148B ILE 3.0 19.7 - - - +
149B ARG* 3.2 59.7 - - + -
150B ASN* 3.4 3.9 + - - -
154B THR* 1.3 76.0 - - - +
156B GLN* 1.3 63.2 + - - +
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Residues in contact with GLN 156 (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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92A PHE* 3.7 7.5 - - - -
93A PRO 3.2 25.5 + - - +
94A LYS* 4.3 6.0 - - - +
95A SER* 5.2 1.2 + - - -
119B VAL 3.2 7.9 - - - -
120B THR* 3.5 31.1 - - + +
122B PHE* 3.3 4.5 - - - -
147B LEU* 3.5 3.1 - - - +
148B ILE* 3.0 60.2 + - + +
150B ASN* 3.2 21.5 + - - +
155B PHE* 1.3 79.0 - - - +
157B VAL* 1.3 65.7 + - - +
158B LEU* 4.1 12.6 - - + +
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Residues in contact with VAL 157 (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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117B CYS 3.6 1.6 - - - +
119B VAL* 2.7 54.3 + - + +
122B PHE* 4.4 11.7 - - + -
127B ILE* 4.8 3.8 - - + -
129B VAL* 4.1 16.2 - - + -
144B SER* 3.8 20.0 - - - +
145B THR* 3.6 22.4 - - - +
146B GLN 4.1 5.8 - - - +
147B LEU* 4.5 5.8 - - + -
148B ILE* 5.2 0.2 - - - -
156B GLN* 1.3 79.4 - - - +
158B LEU* 1.3 69.0 + - - +
159B VAL* 4.6 4.3 - - + -
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Residues in contact with LEU 158 (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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116B VAL* 4.2 13.7 - - + -
117B CYS 3.2 4.5 - - - +
118B SER* 3.4 36.3 - - - +
119B VAL 4.2 0.2 - - - +
120B THR* 4.5 1.3 - - + -
144B SER* 3.6 1.6 + - - -
145B THR* 3.0 45.6 + - + +
148B ILE* 3.9 26.0 - - + -
156B GLN* 4.1 17.5 - - - +
157B VAL* 1.3 93.1 - - - +
159B VAL* 1.3 61.2 + - - +
160B MET* 3.8 7.7 - - + +
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Residues in contact with VAL 159 (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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116B VAL* 3.7 0.2 - - - -
117B CYS* 3.0 35.2 + - + +
119B VAL* 5.2 0.2 - - + -
129B VAL* 4.0 40.4 - - + +
130B ARG 6.1 0.2 - - - -
131B TRP* 3.1 21.7 + - + +
142B VAL* 3.6 31.2 - - + -
143B SER 3.4 9.6 - - - +
144B SER* 3.7 18.6 - - - +
157B VAL* 4.6 7.4 - - + -
158B LEU* 1.3 77.5 - - - +
160B MET* 1.3 61.6 + - - +
173B CYS* 5.9 0.2 - - - -
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Residues in contact with MET 160 (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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114B THR* 3.8 20.9 - - + -
115B LEU 3.3 5.2 - - - -
116B VAL* 4.2 16.8 - - + +
131B TRP* 3.9 0.4 - - - -
141B GLY 4.4 0.7 - - - -
142B VAL* 3.3 8.5 - - - +
143B SER* 2.6 48.7 + - - +
144B SER 5.7 0.4 - - - -
145B THR* 3.7 24.5 - - + +
158B LEU* 3.8 18.4 - - + +
159B VAL* 1.3 81.3 - - - +
161B LEU* 1.3 63.2 + - - +
162B GLU* 4.4 2.2 - - + -
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Residues in contact with LEU 161 (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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113B ASN 3.5 1.2 - - - +
114B THR* 3.3 1.9 - - - +
115B LEU* 2.8 43.6 + - + +
131B TRP* 3.7 39.3 - - + +
132B PHE 5.5 0.9 - - - +
133B ARG* 5.7 1.8 - - + +
138B GLU* 4.0 22.2 - - + -
140B VAL 3.8 22.7 - - - +
141B GLY 3.6 8.1 - - - +
142B VAL* 4.0 4.0 - - + -
160B MET* 1.3 76.6 - - - +
162B GLU* 1.3 77.8 + - - +
163B MET* 3.5 11.1 + - + +
171B TYR* 4.6 19.5 - - + -
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Residues in contact with GLU 162 (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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111B HIS 4.6 3.6 - - - +
112B HIS* 3.2 36.7 - - + +
113B ASN 3.3 6.3 - - - +
114B THR* 3.1 24.7 + - + +
140B VAL 5.3 0.2 - - - +
141B GLY* 3.2 24.2 + - - +
160B MET* 5.8 1.8 - - + -
161B LEU* 1.3 81.9 - - - +
163B MET* 1.3 56.7 + - - +
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Residues in contact with MET 163 (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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2B SER* 6.4 1.8 - - - -
112B HIS* 3.1 11.6 + - - -
113B ASN* 2.7 57.0 + - + +
115B LEU* 3.9 26.9 - - + -
133B ARG* 5.6 4.5 - - - +
161B LEU* 4.4 16.2 - - + +
162B GLU* 1.3 73.6 - - - +
164B THR* 1.3 59.7 + - - +
165B PRO* 3.1 29.9 - - + +
171B TYR* 3.5 41.1 - - + +
188B TRP* 5.4 4.9 - - - +
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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