Contacts of the strand formed by residues 108 - 113 (chain Y) in PDB entry 1IRA
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 108 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34X TYR* 3.6 26.2 - - + -
35X LEU 4.0 9.9 - - - +
36X GLN* 3.4 40.2 - - + -
12Y LEU* 4.3 2.7 - - + -
106Y ALA* 3.4 9.0 - - + -
107Y ILE* 1.3 75.5 - - - +
109Y LYS* 1.3 62.3 + - - +
110Y GLN* 3.7 5.5 + - + +
123Y PRO* 3.8 28.7 - - + -
124Y TYR* 3.6 35.4 - + - -
191Y ARG* 4.5 16.6 - - + -
192Y VAL 3.1 19.8 + - - +
193Y ILE* 3.4 7.2 - - + +
194Y GLU 2.9 23.7 + - - -
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Residues in contact with LYS 109 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X GLN* 4.9 4.0 - - - +
22X THR* 5.8 3.5 - - - +
35X LEU 4.1 9.8 + - - +
36X GLN 6.1 0.2 - - - -
37X GLY* 5.5 10.8 - - - +
40X VAL* 5.0 23.6 - - + -
107Y ILE* 4.4 9.2 - - + +
108Y PHE* 1.3 75.0 - - - +
110Y GLN* 1.3 64.9 + - - +
111Y LYS* 5.4 9.3 + - + +
194Y GLU* 3.2 35.2 + - - +
196Y ILE* 4.1 20.6 - - + +
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Residues in contact with GLN 110 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X GLN* 3.3 35.3 - - + +
34X TYR* 4.3 6.9 - - + -
108Y PHE* 3.7 5.3 + - + +
109Y LYS* 1.3 80.3 - - - +
111Y LYS* 1.3 62.4 + - - +
120Y LEU* 3.2 32.3 - - + +
121Y VAL* 2.8 28.0 + - - +
123Y PRO* 4.2 8.1 - - - +
193Y ILE* 3.2 34.1 - - + +
194Y GLU 3.0 10.7 + - - +
195Y PHE* 3.3 5.8 - - + -
196Y ILE* 2.9 25.6 + - - +
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Residues in contact with LYS 111 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X ARG* 3.4 39.9 - - - +
15X ILE 5.3 0.2 + - - -
16X TRP* 3.3 50.8 + - + +
20X GLN* 2.9 26.9 + - - +
22X THR* 4.6 11.1 - - - +
43X GLU* 4.9 3.8 + - - -
109Y LYS* 5.4 7.8 + - + -
110Y GLN* 1.3 78.5 - - - +
112Y LEU* 1.3 63.3 + - - +
195Y PHE* 4.4 1.1 - - - -
196Y ILE* 3.1 22.9 - - + +
198Y LEU* 4.0 29.8 - - + -
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Residues in contact with LEU 112 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X TRP* 4.8 0.4 - - - -
18X VAL 5.8 0.7 - - - +
20X GLN* 3.5 20.6 - - - +
147X TYR* 3.5 33.4 - - + +
111Y LYS* 1.3 80.9 - - - +
113Y PRO* 1.3 74.8 - - + +
118Y GLY* 3.5 12.1 - - - -
119Y GLY 3.3 34.3 - - - +
120Y LEU* 4.0 5.2 - - + -
163Y VAL* 5.4 0.7 - - + -
166Y VAL* 4.4 9.0 - - + +
195Y PHE* 3.6 31.4 - - + -
196Y ILE 3.2 3.8 + - - -
197Y THR* 3.5 6.4 - - - -
198Y LEU* 2.9 24.5 + - - +
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Residues in contact with PRO 113 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X TRP* 4.7 2.7 - - + -
107X PRO* 4.7 12.8 - - + +
147X TYR* 3.5 39.0 - - + -
149X GLN* 3.7 19.5 - - - +
112Y LEU* 1.3 88.9 - - + +
114Y VAL* 1.3 66.2 - - - +
116Y GLY* 4.3 3.3 + - - +
166Y VAL* 3.8 13.3 - - - +
198Y LEU* 3.3 11.8 - - + +
200Y GLU* 3.9 22.4 - - + +
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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