Contacts of the strand formed by residues 164 - 169 (chain C) in PDB entry 2IHU
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 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C VAL 2.9 8.4 + - - -
103C ILE* 3.5 6.5 - - - +
104C ALA* 2.9 26.6 + - - +
135C TYR* 3.3 23.3 - - - +
152C ALA* 2.7 48.4 + - - -
155C ALA* 3.7 1.2 - - - +
156C ALA* 3.5 12.0 + - - +
162C GLY 4.0 0.2 + - - -
163C PRO* 1.3 73.6 + - - +
165C PHE* 1.3 60.5 + - - +
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Residues in contact with PHE 165 (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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85C MET* 4.0 10.5 - - + -
88C LEU* 5.4 1.3 - - + -
92C ILE* 4.3 9.0 - - + -
104C ALA* 3.2 27.4 - - + -
105C LEU 4.4 0.4 - - - -
106C ALA* 3.6 36.6 - - + -
125C SER* 3.8 41.1 - - - -
126C VAL* 4.2 2.9 - - + -
129C VAL* 3.6 32.1 - - + -
133C SER* 4.8 1.3 - - - +
135C TYR* 2.8 14.3 + - - +
136C ALA* 3.2 13.0 - - + -
137C VAL* 3.0 27.2 + - - +
164C SER* 1.3 73.3 - - - +
166C ILE* 1.3 68.3 + - - +
167C SER* 3.8 21.1 - - - -
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Residues in contact with ILE 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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103C ILE* 4.7 3.6 - - + -
104C ALA 3.0 7.0 + - - +
105C LEU* 3.6 25.5 - - + -
106C ALA 3.2 23.4 + - - +
135C TYR* 4.8 0.2 - - + -
137C VAL* 3.3 21.5 - - + +
139C LEU 4.6 0.9 - - - +
145C ILE* 4.0 9.2 - - + -
148C LEU* 3.9 37.7 - - + +
149C VAL* 4.0 17.9 - - + +
152C ALA* 4.1 13.7 - - + -
165C PHE* 1.3 82.3 - - - +
167C SER* 1.3 65.6 + - - +
168C LEU* 3.6 25.9 - - + +
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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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106C ALA 3.4 6.0 + - - -
107C ALA 4.5 0.7 + - - -
108C GLN* 3.4 29.5 + - - +
125C SER* 4.1 6.8 + - - -
126C VAL* 4.3 5.8 - - - -
137C VAL 2.8 16.2 + - - -
138C GLU* 3.4 14.6 + - - +
139C LEU* 2.9 28.9 + - - +
165C PHE* 3.8 21.2 - - - -
166C ILE* 1.3 72.7 - - - +
168C LEU* 1.3 60.0 + - - +
169C PRO* 3.5 2.7 - - - +
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Residues in contact with LEU 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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18C LEU* 3.8 12.6 - - + -
78C TRP* 3.5 38.4 - - + -
105C LEU* 4.2 13.0 - - + -
106C ALA 2.8 16.5 + - - +
107C ALA* 3.5 5.6 - - - +
108C GLN* 3.0 17.5 + - - +
139C LEU* 4.2 13.5 - - + -
145C ILE* 3.7 19.5 - - + -
166C ILE* 3.6 28.9 - - + +
167C SER* 1.3 76.7 + - - +
169C PRO* 1.3 69.4 - - - +
170C VAL* 3.2 3.3 + - - +
173C LEU* 4.3 19.1 - - + +
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Residues in contact with PRO 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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108C GLN* 3.4 13.9 - - + +
109C SER 3.4 13.2 - - - +
111C SER* 3.7 6.1 - - - +
114C ILE* 4.1 14.4 - - + -
138C GLU* 4.0 13.9 - - + +
139C LEU* 3.5 30.5 - - + +
167C SER 3.5 8.5 - - - +
168C LEU* 1.3 81.6 - - - +
170C VAL* 1.3 59.0 + - - +
171C ASP* 3.2 13.9 - - - +
172C LEU* 3.0 17.3 + - + +
173C LEU* 2.9 24.8 + - - +
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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