Contacts of the strand formed by residues 98 - 105 (chain S) 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 PHE 98 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12S TYR* 3.6 35.4 - + - -
44S PHE* 3.2 5.9 - - - -
45S GLU 2.9 38.7 + - - +
46S THR* 5.6 4.9 - - - -
49S GLY* 4.1 24.7 - - - -
50S PHE* 4.6 7.2 - + - -
67S TRP* 3.5 24.5 - + + -
96S ASN 5.3 1.3 - - - -
97S ALA* 1.3 73.7 - - - +
99S ILE* 1.3 60.1 + - - +
116S ILE* 4.0 3.8 - - + -
118S TYR 3.5 3.8 - - - -
119S LYS* 3.9 14.8 - - + -
120S PRO* 3.7 22.9 - - + -
123S TYR* 3.8 38.4 - + - -
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Residues in contact with ILE 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42S LEU* 4.4 9.4 - - + -
43S GLU 3.4 10.3 - - - +
44S PHE* 4.2 5.2 - - + -
87S LEU* 3.9 18.8 - - + -
90S CYS* 3.7 33.0 - - + -
91S LYS* 3.6 38.4 - - + +
94S TYR 4.3 5.8 - - - +
97S ALA* 4.0 3.6 - - + +
98S PHE* 1.3 80.6 - - - +
100S ARG* 1.3 68.4 + - - +
101S ILE* 5.7 0.2 - - + -
116S ILE* 3.3 5.6 - - - +
117S ALA* 2.8 23.4 + - + -
118S TYR* 2.9 31.9 + - + -
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Residues in contact with ARG 100 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASN* 4.0 22.7 + - - +
183B LYS* 5.7 2.6 - - - +
187B ARG* 5.8 0.4 - - - +
41S CYS 4.0 0.2 - - - +
42S LEU* 3.5 5.7 - - - +
43S GLU* 2.8 63.1 + - + +
65S ARG 3.0 24.4 + - - -
66S TYR* 4.8 0.2 - - - +
67S TRP* 3.3 54.0 - - + +
99S ILE* 1.3 76.6 - - - +
101S ILE* 1.3 64.8 + - - +
102S ILE* 4.1 8.6 + - + +
114S SER* 4.2 15.0 + - - -
115S PHE 3.3 19.7 - - - +
116S ILE* 3.9 8.7 - - + -
117S ALA 4.1 0.4 - - - +
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Residues in contact with ILE 101 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26S LEU* 4.2 11.7 - - + -
30S VAL* 4.4 11.9 - - + -
33S LEU* 4.2 16.8 - - + -
40S PRO* 5.2 0.2 - - + -
41S CYS 3.7 8.7 - - - +
42S LEU* 4.5 13.5 - - + -
83S VAL* 4.4 20.9 - - + -
84S LEU* 5.4 0.9 - - + -
87S LEU* 4.5 13.9 - - + -
100S ARG* 1.3 76.7 - - - +
102S ILE* 1.3 69.7 + - - +
113S VAL 4.2 0.3 - - - -
114S SER* 3.3 3.8 + - - -
115S PHE* 3.0 56.2 + - + -
117S ALA* 3.9 23.3 - - + -
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Residues in contact with ILE 102 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33S LEU* 3.8 7.8 - - - +
40S PRO* 3.3 4.5 - - - +
41S CYS* 2.9 52.3 + - + +
43S GLU* 3.8 36.3 - - + +
100S ARG* 4.2 10.1 - - + +
101S ILE* 1.3 80.9 - - - +
103S GLY* 1.3 59.7 + - - +
104S PHE* 3.6 31.9 - - + -
111S GLN* 3.7 27.6 - - - +
113S VAL 3.1 8.3 - - - +
114S SER* 3.7 14.6 - - - +
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Residues in contact with GLY 103 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33S LEU* 3.8 21.3 - - - -
38S TRP* 4.3 4.7 - - - -
39S VAL 3.2 7.2 - - - -
102S ILE* 1.3 75.9 - - - +
104S PHE* 1.3 63.4 + - - -
111S GLN* 3.3 5.5 - - - -
112S CYS* 3.0 27.9 + - - +
113S VAL* 2.9 15.6 + - - +
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Residues in contact with PHE 104 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B ASN* 4.1 12.6 - - - -
187B ARG* 3.8 31.6 - - - -
38S TRP* 3.3 9.9 - - - -
39S VAL* 2.8 51.9 + - + +
41S CYS* 3.7 26.7 - - + -
69S MET* 5.5 0.4 - - + -
73S PRO* 4.3 20.9 - - + -
75S PHE* 6.2 0.9 - + - -
102S ILE* 3.6 16.8 - - + -
103S GLY* 1.3 74.4 - - - -
105S ASP* 1.3 62.7 + - - +
106S SER* 3.7 5.7 + - - +
109S GLN* 6.0 2.2 - - + -
110S VAL 4.0 4.7 - - - -
111S GLN* 3.7 28.3 - - + -
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Residues in contact with ASP 105 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38S TRP* 3.7 22.2 + - + -
103S GLY 4.1 0.4 + - - -
104S PHE* 1.3 74.0 - - - +
106S SER* 1.3 49.9 + - - +
107S ASN* 2.8 24.2 + - - +
108S ARG* 3.0 29.5 + - - +
109S GLN* 2.6 37.2 + - - -
110S VAL* 3.0 19.0 + - + +
112S CYS* 3.6 18.6 - - - -
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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