Contacts of the strand formed by residues 110 - 118 (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 VAL 110 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C ILE* 5.7 0.2 - - + -
156C GLN* 3.6 28.7 - - + -
159C ARG* 4.3 18.8 - - + +
160C ASP* 5.7 3.1 - - - -
165C TYR* 4.8 3.1 - - + -
104U PHE* 4.9 3.1 - - - -
105U ASP* 3.0 27.3 + - - +
108U ARG* 3.6 50.5 - - + +
109U GLN* 1.3 82.8 - - - +
111U GLN* 1.3 78.1 + - - +
112U CYS* 3.3 5.5 + - - -
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Residues in contact with GLN 111 (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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159C ARG* 5.0 1.2 - - - -
160C ASP* 5.4 1.5 + - - +
165C TYR* 3.1 67.7 - - + +
166C GLY 4.6 0.2 + - - -
183D LYS* 3.7 9.5 - - + +
187D ARG* 3.1 33.0 + - - +
43U GLU* 5.0 1.9 + - - +
100U ARG* 6.4 0.4 - - - -
102U ILE* 3.9 31.2 - - + +
103U GLY 3.3 9.4 - - - +
104U PHE* 3.7 21.8 - - + +
110U VAL* 1.3 77.0 - - - +
112U CYS* 1.3 59.1 + - - +
113U VAL 3.4 5.4 - - - +
114U SER* 4.4 1.4 + - - -
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Residues in contact with CYS 112 (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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166C GLY* 3.3 22.9 - - - +
396C ASP* 4.5 7.2 - - - +
32U TYR* 5.4 1.2 - - - -
38U TRP* 3.7 41.5 - - + -
103U GLY 2.9 6.8 + - - +
105U ASP* 3.7 31.9 - - - -
108U ARG* 4.0 20.0 - - - -
110U VAL* 3.3 6.0 + - - -
111U GLN* 1.3 74.8 - - - +
113U VAL* 1.3 64.7 + - - +
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Residues in contact with VAL 113 (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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165C TYR* 4.8 1.3 - - - -
166C GLY* 4.7 2.7 - - - -
432C ASN* 6.0 0.4 - - - +
29U GLN* 5.4 4.5 - - - +
32U TYR* 4.1 15.0 - - + -
33U LEU* 4.2 22.0 - - + -
38U TRP* 3.6 28.9 - - + -
101U ILE 4.3 2.2 - - - +
102U ILE* 3.1 5.0 - - - +
103U GLY* 2.9 31.6 + - - +
111U GLN* 3.4 4.2 - - - +
112U CYS* 1.3 86.3 - - - +
114U SER* 1.3 70.0 + - - +
115U PHE* 3.7 29.6 - - + -
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Residues in contact with SER 114 (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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165C TYR* 4.0 35.7 + - - +
166C GLY* 5.1 1.0 - - - -
13U GLU* 5.4 2.9 - - - +
14U THR* 3.7 22.4 + - - +
100U ARG* 4.2 12.3 + - - -
101U ILE 3.3 7.9 - - - -
102U ILE* 3.7 16.3 - - - +
111U GLN* 4.4 1.1 + - - -
113U VAL* 1.3 80.0 - - - +
115U PHE* 1.3 65.1 + - - +
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Residues in contact with PHE 115 (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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12U TYR 5.2 2.9 - - - -
14U THR* 3.6 19.7 - - + +
15U LEU* 4.0 16.4 - - + -
21U LEU* 4.2 15.9 - - + -
26U LEU* 3.5 29.6 - - + -
29U GLN* 3.8 28.3 - - + -
30U VAL* 4.8 4.9 - - + -
33U LEU* 5.7 0.9 - - + -
100U ARG* 3.3 5.7 - - - +
101U ILE* 3.0 58.8 + - + -
113U VAL* 3.7 28.9 - - + -
114U SER* 1.3 75.7 + - - +
116U ILE* 1.3 73.6 + - - +
117U ALA* 4.4 2.9 - - + -
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Residues in contact with ILE 116 (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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12U TYR* 3.6 48.8 + - + +
14U THR 5.0 1.0 + - - -
21U LEU* 5.2 4.0 - - - +
67U TRP* 4.1 24.0 - - + -
98U PHE* 4.9 3.4 - - + -
99U ILE 3.7 9.2 - - - +
100U ARG* 4.0 13.7 - - + +
115U PHE* 1.3 81.4 - - - +
117U ALA* 1.3 60.5 + - - +
118U TYR 3.9 9.4 - - - +
119U LYS* 3.5 36.3 - - + -
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Residues in contact with ALA 117 (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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21U LEU* 6.3 0.2 - - - -
26U LEU* 4.4 12.2 - - + +
87U LEU* 4.2 22.6 - - + +
91U LYS* 5.8 0.5 + - - +
99U ILE 2.8 10.9 + - - +
101U ILE* 3.9 34.5 - - + -
115U PHE* 3.4 9.3 + - + +
116U ILE* 1.3 75.3 - - - +
118U TYR* 1.3 61.2 + - - +
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Residues in contact with TYR 118 (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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87U LEU* 4.7 1.8 - - + -
91U LYS* 3.7 39.7 - - + -
94U TYR 4.2 4.5 - - - -
95U PRO* 2.7 38.4 + - + +
97U ALA 3.2 27.4 - - - -
98U PHE* 3.6 2.6 - - - +
99U ILE* 3.0 50.5 + - + +
116U ILE* 3.6 3.1 - - - +
117U ALA* 1.3 82.0 - - - +
119U LYS* 1.3 88.5 + - - +
120U PRO* 4.2 2.4 - - - +
121U ALA 4.9 1.6 + - - -
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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