Contacts of the strand formed by residues 129 - 134 (chain I) in PDB entry 2IAN
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 129 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119I GLN* 3.4 26.6 + - - +
120I LEU 3.2 17.7 - - - -
121I ARG* 4.1 11.4 - - - -
127I ASP 3.7 4.7 + - - -
128I LYS* 1.3 76.2 - - - +
130I VAL* 1.3 71.9 + - - +
131I CYS* 5.6 0.3 - - - -
173I TRP* 4.1 10.4 - - - +
174I SER 5.0 4.7 - - - +
179I PHE* 6.1 0.3 - - - -
181I CYS* 5.3 0.3 - - - -
124J PHE* 3.5 8.2 - - - -
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Residues in contact with VAL 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I TYR 3.6 0.7 - - - +
119I GLN* 3.4 5.4 - - - +
120I LEU* 2.8 41.4 + - + +
129I SER* 1.3 85.0 + - - +
131I CYS* 1.3 68.2 + - - +
171I VAL* 3.8 20.9 - - + -
172I ALA 3.8 4.7 - - - +
173I TRP* 4.0 9.6 - - + +
179I PHE* 6.3 0.7 - - - -
124J PHE* 3.9 20.2 - - + -
140J VAL* 4.2 18.4 - - + -
142J LEU* 3.7 32.5 - - + -
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Residues in contact with CYS 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I VAL* 4.2 3.4 - - + -
118I TYR 3.4 3.6 - - - -
129I SER* 5.6 0.9 - - - -
130I VAL* 1.3 75.3 - - - +
132I LEU* 1.3 59.9 + - - +
133I PHE 3.9 0.8 + - - -
170I ALA 3.9 0.3 - - - +
171I VAL* 3.5 6.4 - - - +
172I ALA* 2.9 40.1 + - + +
179I PHE* 3.9 24.0 - - - -
181I CYS* 2.1 57.7 - - + -
184I ALA* 4.1 0.2 - - - -
185I PHE* 4.1 19.3 - - + -
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Residues in contact with LEU 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I ALA 3.7 0.2 - - - +
117I VAL* 3.3 3.4 - - - -
118I TYR* 2.8 42.4 + - + +
120I LEU* 3.7 23.1 - - + -
130I VAL* 4.0 1.0 + - + -
131I CYS* 1.3 70.6 - - - +
133I PHE* 1.3 59.5 + - - +
134I THR* 3.6 27.7 + - + +
169I SER* 4.1 22.7 - - - -
170I ALA 3.7 2.5 - - - +
171I VAL* 4.0 16.8 - - + -
130J GLU* 4.7 2.0 - - - +
138J THR* 3.6 32.1 - - + +
140J VAL* 3.9 23.6 - - + -
189J ARG* 4.2 6.1 - - + -
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Residues in contact with PHE 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I PRO* 4.4 4.7 - - + -
116I ALA 3.2 22.2 - - - -
117I VAL* 3.6 12.8 - - + -
131I CYS 3.9 2.4 + - - -
132I LEU* 1.3 71.3 - - - +
134I THR* 1.3 59.5 + - - +
136I PHE* 3.5 39.9 - + + -
140I THR* 4.2 11.2 - - + -
142I VAL* 4.5 11.4 - - + -
169I SER* 3.4 1.6 - - - -
170I ALA* 2.7 38.7 + - + +
185I PHE* 3.4 46.9 - + + -
188I SER* 5.8 4.0 - - - -
189I ILE 5.6 1.3 - - - -
190I ILE* 5.3 7.6 - - + -
191I PRO* 4.0 22.9 - - + -
194I THR* 4.0 18.8 - - + -
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Residues in contact with THR 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I PRO* 3.6 0.7 - - - +
116I ALA 3.1 26.6 + - - +
118I TYR* 3.8 28.3 - - + -
132I LEU* 3.6 33.9 - - + +
133I PHE* 1.3 75.0 - - - +
135I ASP* 1.3 93.3 + - - +
136I PHE* 3.4 7.5 + - - -
167I SER* 4.5 0.3 + - - -
168I ASN 3.3 12.9 + - - -
169I SER* 4.4 5.6 - - - -
130J GLU* 4.9 0.4 - - - +
138J THR* 5.8 0.4 - - - -
191J ARG* 3.4 14.3 + - - +
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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