Contacts of the strand formed by residues 114 - 122 (chain F) in PDB entry 1R5I
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 LEU 114 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F PRO* 3.7 2.8 - - - +
104F SER* 3.1 50.0 + - - +
105F LYS 4.0 2.0 - - - +
106F THR* 3.0 38.1 - - - +
112F HIS 4.9 1.8 - - - +
113F ASN* 1.3 78.5 - - + +
115F LEU* 1.3 61.5 + - - +
116F VAL* 4.0 0.4 + - + -
143F VAL* 5.8 3.1 - - + -
160F MET* 3.5 44.0 - - + -
161F LEU 2.9 23.6 - - - +
162F GLU* 3.9 15.7 - - + -
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Residues in contact with LEU 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F VAL* 4.5 4.3 - - + -
102F TYR 4.0 1.3 - - - -
103F PRO* 4.1 19.3 - - + -
112F HIS 6.1 0.4 - - - +
114F LEU* 1.3 73.9 - - - +
116F VAL* 1.3 60.1 + - - +
131F TRP* 3.9 21.1 - - + -
160F MET* 3.2 4.5 - - - +
161F LEU* 2.9 36.7 + - + +
163F THR* 4.9 9.2 - - - +
165F PRO* 5.4 7.4 - - + -
171F TYR* 3.5 48.5 - - + -
188F TRP* 3.7 42.6 - - + +
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Residues in contact with VAL 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F THR 3.7 0.2 - - - +
101F VAL* 3.3 6.1 - - - +
102F TYR* 2.9 70.5 + - + +
104F SER* 3.7 27.4 - - - -
114F LEU* 4.5 2.0 - - + +
115F LEU* 1.3 76.1 - - - +
117F CYS* 1.3 63.9 + - - +
118F SER 3.7 1.2 + - - -
131F TRP* 4.2 2.5 - - - -
158F LEU* 4.0 21.3 - - + -
160F MET* 3.6 31.4 - - + -
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Residues in contact with CYS 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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99F VAL* 3.7 20.0 - - - -
100F THR 3.7 2.2 - - - -
101F VAL* 4.3 3.4 - - - -
116F VAL* 1.3 73.6 - - - +
118F SER* 1.3 58.7 + - - +
119F VAL* 3.7 12.8 + - - +
129F VAL* 4.3 0.4 - - - -
131F TRP* 3.5 14.5 - - + +
157F THR 3.7 0.5 - - - +
158F LEU* 3.5 4.2 - - - -
159F VAL* 2.9 43.9 + - + +
173F CYS* 2.0 50.0 - - + -
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Residues in contact with SER 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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96E PRO* 3.2 26.9 - - - +
98F LYS 3.3 1.9 + - - +
99F VAL* 3.2 5.9 - - - +
100F THR* 2.8 51.6 + - - +
102F TYR* 4.0 17.7 - - - -
116F VAL 3.7 1.8 + - - -
117F CYS* 1.3 71.1 - - - +
119F VAL* 1.3 62.1 + - - +
120F SER* 4.1 7.6 + - - -
158F LEU* 3.9 17.0 - - - +
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Residues in contact with VAL 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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97F PRO* 3.7 20.4 - - + -
98F LYS 3.5 2.5 - - - -
99F VAL* 4.1 8.5 - - + -
117F CYS* 4.0 17.5 - - - +
118F SER* 1.3 78.4 + - - +
120F SER* 1.3 58.1 + - - +
122F PHE* 3.5 19.7 - - + -
127F ILE* 3.7 13.7 - - + -
129F VAL* 4.1 11.7 - - + -
156F GLN* 3.2 3.6 - - - -
157F THR* 2.9 42.9 + - + +
158F LEU* 4.6 0.8 - - - +
159F VAL* 5.5 0.2 - - + -
175F VAL* 3.8 23.8 - - + -
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Residues in contact with SER 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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94E ASN 3.7 20.9 - - - -
95E SER* 3.7 20.7 - - - -
96E PRO* 4.3 1.1 - - - +
96F GLU 4.6 0.2 - - - +
97F PRO* 3.4 1.4 - - - +
98F LYS* 2.9 48.8 + - - +
118F SER* 4.1 9.2 + - - -
119F VAL* 1.3 76.2 - - - +
121F GLY* 1.3 65.6 + - - +
122F PHE* 3.3 5.3 + - - -
155F PHE 3.8 4.5 - - - -
156F GLN* 3.9 10.1 - - - -
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Residues in contact with GLY 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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94E ASN* 5.0 2.7 + - - -
95F VAL* 3.2 24.8 - - - +
96F GLU 4.0 5.1 - - - +
120F SER* 1.3 76.3 - - - +
122F PHE* 1.3 59.1 + - - +
150F ASN* 5.0 1.4 - - - +
154F THR* 4.1 21.1 - - - +
155F PHE 3.0 9.6 + - - -
156F GLN* 4.6 0.6 - - - +
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Residues in contact with PHE 122 (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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95F VAL* 3.2 11.2 - - - +
97F PRO* 3.3 36.8 - - + -
119F VAL* 3.5 33.7 - - + -
120F SER 3.3 1.3 - - - -
121F GLY* 1.3 77.8 - - - +
123F TYR* 1.3 64.3 + - - +
124F PRO 3.2 26.2 - - - -
125F GLY 3.8 13.9 - - - -
127F ILE* 3.8 18.8 - - + -
147F LEU* 3.7 13.5 - - + -
154F THR* 3.4 2.4 - - - -
155F PHE* 2.8 60.3 + - + -
156F GLN* 3.8 2.7 - - - -
157F THR* 4.0 7.0 - - + -
177F HIS* 3.7 9.6 - + - +
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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