Contacts of the strand formed by residues 98 - 105 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12U TYR* 3.5 39.3 - + - -
44U PHE* 3.1 5.5 - - - -
45U GLU* 3.0 40.1 + - + +
46U THR 5.5 5.2 - - - -
47U ASP 5.9 0.7 - - - -
49U GLY* 4.0 23.6 - - - -
50U PHE* 4.4 8.3 - + - -
67U TRP* 3.5 25.0 - + + -
96U ASN 5.4 0.7 - - - -
97U ALA* 1.3 74.8 - - - +
99U ILE* 1.3 61.8 + - - +
116U ILE* 4.9 2.7 - - + -
118U TYR 3.6 4.9 - - - +
119U LYS* 4.1 10.3 - - + -
120U PRO* 3.8 22.7 - - + -
123U TYR* 3.8 39.9 - + + -
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Residues in contact with ILE 99 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42U LEU* 4.5 9.6 - - + -
43U GLU 3.4 11.0 - - - +
44U PHE* 4.2 4.5 - - + -
67U TRP* 4.4 1.3 - - - -
87U LEU* 3.8 18.6 - - + -
90U CYS* 3.6 35.4 - - + +
91U LYS* 3.6 36.6 - - + +
94U TYR 4.4 4.5 - - - +
97U ALA* 4.0 4.5 - - + +
98U PHE* 1.3 80.1 - - - +
100U ARG* 1.3 69.3 + - - +
116U ILE* 3.7 2.9 - - - +
117U ALA* 2.8 23.1 + - + -
118U TYR* 3.0 33.1 + - + +
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Residues in contact with ARG 100 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C ASN* 4.0 22.4 + - - +
183D LYS* 5.8 1.2 - - - +
41U CYS 4.0 0.2 - - - +
42U LEU* 3.5 6.1 - - - +
43U GLU* 2.8 62.0 + - + +
65U ARG 3.1 23.2 + - - -
67U TRP* 3.4 59.2 - - + +
99U ILE* 1.3 77.6 - - - +
101U ILE* 1.3 64.1 + - - +
102U ILE* 4.1 8.2 + - + +
111U GLN* 6.4 0.4 - - - -
114U SER* 4.2 15.2 + - - -
115U PHE 3.3 19.5 - - - +
116U ILE* 4.0 11.0 - - + +
117U ALA 4.1 0.4 - - - +
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Residues in contact with ILE 101 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26U LEU* 4.5 4.7 - - + -
30U VAL* 4.4 16.4 - - + -
33U LEU* 4.2 17.3 - - + -
40U PRO* 5.2 0.4 - - + -
41U CYS 3.7 8.5 - - - +
42U LEU* 4.5 14.6 - - + -
83U VAL* 4.6 19.7 - - + -
84U LEU* 5.3 1.6 - - + -
87U LEU* 4.6 13.9 - - + -
100U ARG* 1.3 77.3 - - - +
102U ILE* 1.3 70.5 + - - +
113U VAL* 4.2 0.3 - - - +
114U SER* 3.3 3.8 + - - -
115U PHE* 3.0 57.3 + - + +
117U ALA* 3.9 24.5 - - + -
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Residues in contact with ILE 102 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D ARG* 4.3 0.2 - - - +
33U LEU* 3.8 7.0 - - - +
40U PRO* 3.4 4.5 - - - +
41U CYS* 2.9 48.8 + - + +
43U GLU* 3.8 37.2 - - + +
100U ARG* 4.2 9.9 - - + +
101U ILE* 1.3 81.8 - - - +
103U GLY* 1.3 59.2 + - - +
104U PHE* 3.5 31.9 - - + -
111U GLN* 3.9 24.9 - - + +
113U VAL 3.1 9.6 - - - +
114U SER* 3.7 18.4 - - - +
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Residues in contact with GLY 103 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33U LEU* 3.8 21.3 - - - -
38U TRP* 4.2 4.7 - - - -
39U VAL 3.4 6.3 - - - -
102U ILE* 1.3 75.7 - - - +
104U PHE* 1.3 62.9 + - - -
111U GLN* 3.3 4.6 - - - -
112U CYS* 2.9 29.8 + - - +
113U VAL* 2.9 18.5 + - - +
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Residues in contact with PHE 104 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D ASN* 4.2 11.2 - - - -
187D ARG* 3.5 36.3 - - - -
38U TRP* 3.2 9.8 - - - -
39U VAL* 2.8 64.5 + - + +
41U CYS* 3.8 26.2 - - + -
69U MET* 5.5 0.7 - - + -
73U PRO* 4.1 15.0 - - + -
75U PHE* 6.2 0.9 - + - -
102U ILE* 3.5 16.8 - - + -
103U GLY* 1.3 74.3 - - - -
105U ASP* 1.3 63.5 + - - +
106U SER* 3.7 2.8 + - - +
109U GLN* 6.1 1.6 - - - -
110U VAL 4.0 3.8 - - - -
111U GLN* 3.7 24.2 - - + -
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Residues in contact with ASP 105 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37U LYS 5.9 0.2 - - - -
38U TRP* 3.5 24.3 + - + -
103U GLY 4.0 0.4 + - - -
104U PHE* 1.3 72.9 - - - +
106U SER* 1.3 52.4 + - - +
107U ASN* 3.1 25.7 + - - +
108U ARG* 3.3 29.6 + - + +
109U GLN* 2.6 36.0 + - - -
110U VAL 3.0 19.4 + - - +
112U CYS* 3.7 17.0 - - - -
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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