Contacts of the strand formed by residues 36 - 44 (chain C) in PDB entry 1IR1
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 ILE 36 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C THR 5.0 1.1 - - - +
35C ASP* 1.3 72.7 - - - +
37C LEU* 1.3 66.6 + - - +
102C ALA* 3.6 0.9 - - - -
103C TYR* 2.8 43.4 + - + +
105C LEU* 5.7 2.0 - - + -
108C PHE* 3.4 41.7 - - + -
116C MET* 4.4 9.4 - - - -
120C ILE* 4.1 22.4 - - + -
138C LEU* 4.4 9.4 - - + -
139C ARG 3.4 10.3 - - - +
140C ILE* 5.2 2.7 - - + -
141C PRO* 3.4 21.3 - - + -
144C TYR* 3.9 26.0 - - + -
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Residues in contact with LEU 37 (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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31C THR* 3.6 34.3 - - + +
35C ASP* 3.9 13.9 - - + -
36C ILE* 1.3 73.5 - - - +
38C ALA* 1.3 62.3 + - - +
85C TYR* 3.7 17.0 - - - +
101C VAL 3.4 2.0 - - - -
102C ALA* 3.7 19.5 - - + -
138C LEU* 3.2 7.8 - - - +
139C ARG* 2.7 71.6 + - + +
364C PHE* 3.7 26.8 - - + -
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Residues in contact with ALA 38 (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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37C LEU* 1.3 76.2 - - - +
39C ALA* 1.3 60.2 + - - +
40C PHE* 3.8 20.2 - - + -
99C CYS 3.6 1.2 - - - +
100C TYR* 3.3 6.1 - - - -
101C VAL* 2.8 34.0 + - + +
103C TYR* 3.8 23.3 - - + -
120C ILE* 4.5 0.4 - - + -
135C LEU* 4.0 2.9 - - + -
137C ASP 3.6 4.7 - - - -
138C LEU* 3.6 18.6 - - + -
364C PHE* 3.8 4.2 - - - -
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Residues in contact with ALA 39 (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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38C ALA* 1.3 71.1 - - - +
40C PHE* 1.3 60.5 + - - +
98C ILE* 4.4 4.5 - - + -
99C CYS 3.7 4.5 - - - -
100C TYR* 4.2 8.1 - - + -
135C LEU* 3.7 2.9 - - - +
136C GLU* 2.9 28.4 + - + +
137C ASP 3.1 11.8 + - - +
363C TYR* 3.9 31.9 - - + -
364C PHE* 3.7 20.4 - - + -
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Residues in contact with PHE 40 (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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38C ALA* 3.8 17.7 - - + -
39C ALA* 1.3 73.8 - - - +
41C ARG* 1.3 60.6 + - - +
42C VAL* 3.4 16.3 + - + +
57C VAL* 3.7 22.0 - - + -
97C TYR 3.4 1.4 - - - +
98C ILE* 3.2 7.3 - - - -
99C CYS* 2.8 41.3 + - + +
101C VAL* 4.2 16.4 - - + -
103C TYR* 3.5 18.6 - - - -
120C ILE* 3.6 36.3 - - + -
124C VAL* 4.8 0.4 - - + -
125C PHE* 4.2 5.2 - + - -
133C LEU* 3.9 31.2 - - + -
134C ARG 3.4 5.6 - - - -
135C LEU* 3.8 22.7 - - + -
136C GLU* 5.3 0.2 - - - -
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Residues in contact with ARG 41 (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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39C ALA 4.1 0.4 + - - -
40C PHE* 1.3 70.3 - - - +
42C VAL* 1.3 58.8 + - - +
43C SER* 4.1 1.1 + - - +
90C VAL* 3.8 15.7 - - + +
96C GLN* 2.9 43.9 + - + +
97C TYR 3.4 3.4 - - - -
98C ILE* 3.9 16.5 - - + +
132C ALA 4.6 0.2 - - - -
133C LEU* 3.5 6.1 - - - +
134C ARG* 2.7 39.1 + - + +
136C GLU* 2.9 37.3 + - + +
305C LYS* 3.1 58.3 + - - +
306C ASN* 4.5 6.1 - - - +
363C TYR* 3.8 12.5 + - - -
474C THR 5.1 0.8 + - - -
475C VAL* 4.1 9.9 + - - -
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Residues in contact with VAL 42 (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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40C PHE* 3.7 14.8 - - + +
41C ARG* 1.3 76.3 - - - +
43C SER* 1.3 65.2 + - - +
44C PRO* 3.5 9.5 - - + +
53C ALA* 4.1 18.8 - - + +
54C GLY* 5.3 0.2 - - - -
57C VAL* 4.9 6.7 - - + -
96C GLN* 3.4 4.3 - - - -
97C TYR* 2.6 42.2 + - + +
99C CYS* 3.7 29.4 - - + -
130C LEU* 4.0 26.2 - - + -
133C LEU* 3.7 21.1 - - + -
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Residues in contact with SER 43 (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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41C ARG* 5.0 1.4 + - - +
42C VAL* 1.3 72.8 - - - +
44C PRO* 1.3 60.4 - - - +
95C ASN 3.9 3.8 - - - -
96C GLN* 3.5 27.9 + - - +
130C LEU* 3.7 1.5 - - - -
131C ARG* 2.7 54.1 + - - +
132C ALA* 3.1 35.5 + - - +
306C ASN* 4.8 3.5 + - - +
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Residues in contact with PRO 44 (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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42C VAL* 3.5 11.7 - - + +
43C SER* 1.3 84.4 - - - +
45C GLN* 1.3 64.7 + - - +
48C VAL* 3.5 27.1 - - + +
50C PRO* 4.6 4.0 - - + -
53C ALA* 3.9 24.9 - - + -
95C ASN* 3.4 27.7 - - - +
97C TYR* 4.1 18.8 - - + -
129C ALA 3.9 6.1 - - - +
130C LEU* 4.4 4.5 - - + -
131C ARG* 3.1 24.5 + - - -
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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