Contacts of the strand formed by residues 165 - 173 (chain C) in PDB entry 2IAM
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 165 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ILE* 6.4 1.3 - - + -
112C ASN 6.1 0.4 - - - -
135C ASP* 5.0 5.4 - - + -
158C LEU 4.0 0.3 - - - +
159C ASP* 3.7 1.8 + - - -
160C MET* 2.8 47.4 + - + +
163C MET* 3.8 20.9 - - + +
164C ASP* 1.3 75.9 - - - +
166C LYS* 1.3 69.4 + - - +
167C SER* 3.8 30.3 - - - -
134D THR* 6.0 0.9 - - + -
136D LYS* 2.8 45.1 - - + -
191D ARG* 3.9 10.3 - - - -
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Residues in contact with LYS 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU* 2.8 31.8 + - - +
77C GLN* 5.0 9.7 - - - +
78C THR* 4.2 17.0 - - + +
108C PRO* 4.2 15.7 - - + -
110C ILE* 3.7 17.5 - - + +
157C VAL* 4.0 20.0 - - + -
158C LEU 3.2 7.6 - - - +
159C ASP* 3.6 30.6 + - + +
164C ASP* 4.3 11.8 + - - -
165C PHE* 1.3 90.5 - - - +
167C SER* 1.3 60.6 + - - +
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Residues in contact with SER 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ILE* 4.0 5.8 - - - -
134C THR* 3.9 2.3 + - - -
135C ASP* 3.7 11.2 - - - -
156C CYS 3.8 1.0 - - - +
157C VAL* 3.6 1.5 - - - -
158C LEU* 2.8 53.7 + - - +
165C PHE* 3.8 8.7 - - - -
166C LYS* 1.3 74.5 - - - +
168C ASN* 1.3 65.0 + - - +
169C SER* 5.0 0.5 - - - -
191D ARG* 2.9 32.4 + - - -
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Residues in contact with ASN 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C PRO* 3.1 26.7 - - - +
110C ILE* 3.2 15.1 - - - +
134C THR* 3.0 5.4 + - - -
135C ASP 2.9 26.4 + - - +
136C PHE* 3.0 43.6 + - + +
137C ASP 3.9 1.2 - - - -
138C SER* 3.3 18.6 + - - -
155C LYS* 4.8 12.8 - - + +
156C CYS 3.5 6.1 - - - +
157C VAL* 3.4 16.2 - - - +
167C SER* 1.3 71.4 - - - +
169C SER* 1.3 61.5 + - - +
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Residues in contact with SER 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C LEU* 4.1 13.0 - - - -
133C PHE 3.1 9.9 - - - -
134C THR* 3.6 15.5 - - - -
136C PHE* 3.7 5.6 - - - -
155C LYS* 3.2 1.9 - - - -
156C CYS 3.0 25.7 + - - -
158C LEU* 4.7 7.1 - - - +
167C SER* 5.0 2.5 - - - -
168C ASN* 1.3 77.3 - - - +
170C ALA* 1.3 61.0 + - - +
138D THR* 5.8 1.8 - - - -
189D ARG* 2.9 40.2 + - - +
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Residues in contact with ALA 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C CYS 3.8 0.2 - - - +
132C LEU* 3.6 7.6 - - - +
133C PHE* 2.6 38.4 + - + +
136C PHE* 4.5 0.9 - - + -
142C VAL* 3.9 35.4 - - + -
153C THR* 4.1 9.0 - - - +
155C LYS* 4.4 4.0 - - - +
169C SER* 1.3 73.9 - - - +
171C VAL* 1.3 67.1 + - - +
185C PHE* 4.0 13.2 - - + -
189D ARG* 3.5 3.4 - - - +
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Residues in contact with VAL 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C VAL* 3.1 37.2 - - + -
131C CYS 3.5 4.5 - - - +
132C LEU* 4.6 5.6 - - + -
151C TYR 3.5 2.1 - - - +
152C ILE* 3.3 3.5 - - - -
153C THR* 2.9 44.2 + - + +
170C ALA* 1.3 75.5 - - - +
172C ALA* 1.3 59.8 + - - +
173C TRP* 4.3 6.7 - - + -
185C PHE* 4.5 1.6 - - - -
140D VAL* 4.2 18.2 - - + -
142D LEU* 4.9 1.6 - - + -
187D SER* 3.6 14.1 - - - +
189D ARG* 3.2 38.6 - - + +
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Residues in contact with ALA 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C VAL* 3.5 1.1 - - - +
131C CYS* 2.7 36.6 + - - +
150C VAL* 5.4 0.2 - - + -
151C TYR 3.1 8.1 - - - +
152C ILE* 3.9 15.9 - - + -
171C VAL* 1.3 75.4 - - - +
173C TRP* 1.3 61.8 + - - +
179C PHE* 3.9 7.0 - - + -
184C ALA* 4.2 16.6 - - + +
185C PHE* 3.7 26.4 - - + -
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Residues in contact with TRP 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C SER 3.9 16.2 - - - +
130C VAL* 4.1 6.7 - - + -
150C VAL* 3.7 0.5 - - - +
151C TYR* 3.0 69.9 + + + -
153C THR* 3.8 28.9 - - + -
171C VAL* 4.3 7.9 - - + -
172C ALA* 1.3 78.9 - - - +
174C SER* 1.3 75.8 + - - +
175C ASN* 5.7 2.9 - - - +
179C PHE* 3.5 10.9 - - - -
142D LEU* 3.4 43.8 - - + +
144D THR* 4.3 13.8 - - + +
173D LEU* 4.6 5.2 - - + -
175D GLU* 5.8 0.9 - - + -
185D ALA* 3.9 29.2 - - + -
186D LEU 4.9 3.6 - - - -
187D SER* 4.8 0.7 - - - -
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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