Contacts of the strand formed by residues 115 - 121 (chain F) in PDB entry 3IT8
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 GLY 115 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111F GLU* 4.2 2.0 - - - -
112F THR* 2.8 34.0 + - - +
113F ALA 3.3 1.2 + - - -
114F ASN* 1.3 81.4 - - - +
116F PRO* 1.3 80.5 - - - +
117F LEU* 3.4 1.2 + - - +
243F TYR* 5.0 0.4 - - - -
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Residues in contact with PRO 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F GLU* 3.9 9.4 - - + -
115F GLY* 1.3 85.6 - - - +
117F LEU* 1.3 63.3 + - - +
130F MET* 3.7 28.0 - - + -
131F THR* 3.6 20.3 + - - +
242F ASN* 4.0 27.1 - - + +
243F TYR* 3.1 38.6 - - + +
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Residues in contact with LEU 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F ILE* 4.1 20.4 - - + -
86F THR* 5.8 4.7 - - + -
110F VAL* 2.9 28.1 + - + +
111F GLU* 4.4 3.6 - - - -
112F THR* 4.1 17.7 - - - +
115F GLY 3.4 2.9 + - - +
116F PRO* 1.3 76.4 - - - +
118F ALA* 1.3 61.8 + - - +
129F LYS* 3.9 3.3 - - - -
130F MET* 3.1 24.0 + - - +
131F THR* 4.4 2.1 + - - -
134F GLY 4.1 11.3 - - - +
135F PHE* 3.7 30.4 - - + +
136F PRO* 4.2 9.9 - - + -
141F LEU* 4.0 23.8 - - + -
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Residues in contact with ALA 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F TYR* 3.2 1.9 - - - -
110F VAL* 2.7 35.4 + - + -
117F LEU* 1.3 80.2 - - + +
119F ARG* 1.3 59.3 + - - +
127F PHE* 3.7 25.1 - - + -
128F THR 3.4 7.0 - - - +
130F MET* 3.2 6.7 - - - +
135F PHE* 3.7 30.3 - - + -
141F LEU* 4.2 8.3 - - + -
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Residues in contact with ARG 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F GLY 4.4 5.2 - - - +
109F TYR* 3.8 6.3 - - + -
118F ALA* 1.3 74.5 - - - +
120F TYR* 1.3 68.5 + - - +
121F HIS* 3.5 33.6 + - + +
127F PHE* 3.3 2.6 - - - -
128F THR* 2.7 39.7 + - - +
129F LYS 4.4 4.2 + - - -
130F MET* 3.4 38.4 - - + +
242F ASN 2.9 24.9 + - - -
243F TYR* 3.7 0.2 - - - +
244F GLU* 3.3 28.8 + - - +
247F GLU* 2.8 42.3 + - - +
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Residues in contact with TYR 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F GLY 2.8 20.7 + - - +
119F ARG* 1.3 75.9 - - - +
121F HIS* 1.3 72.0 + - - +
122F THR* 4.2 8.5 - - - -
125F LYS* 3.6 24.6 - - - +
126F ARG* 3.7 28.5 - - - -
127F PHE* 3.7 28.8 - + + -
148F TRP* 4.1 12.1 - + - -
151F VAL* 5.2 1.3 - - + -
152F LYS* 3.8 22.2 + - + +
155F LEU* 3.9 12.8 - - + -
156F GLY* 3.3 33.4 - - - -
159F GLU* 3.1 39.0 - - - +
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Residues in contact with HIS 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F ARG* 3.5 32.7 + - - +
120F TYR* 1.3 77.4 + - - +
122F THR* 1.3 60.0 + - - +
123F GLY 4.4 2.0 - - - +
124F ASP* 3.7 24.9 - - + +
125F LYS* 2.9 31.4 + - - -
126F ARG 3.0 13.4 + - - +
128F THR* 3.0 37.3 + - + +
244F GLU* 4.7 8.3 - - - -
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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