Contacts of the strand formed by residues 120 - 124 (chain B) in PDB entry 4IRX
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 ALA 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B LYS 2.9 14.4 + - - +
96B VAL* 3.3 7.6 - - + +
97B VAL 3.0 25.6 + - - +
115B VAL* 5.0 2.2 - - - -
118B GLY 3.9 2.2 + - - -
119B VAL* 1.3 73.3 - - - +
121B VAL* 1.3 62.6 + - - +
294B LYS* 3.8 26.0 - - - +
301B LEU* 3.6 22.4 - - + -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 6.1 0.7 - - + -
97B VAL* 3.5 9.0 - - + +
99B VAL* 4.3 18.2 - - + -
111B ALA* 4.2 17.3 - - + +
114B LEU* 3.7 41.3 - - + -
115B VAL* 4.2 11.1 - - + +
119B VAL 3.6 3.8 + - - +
120B ALA* 1.3 79.2 - - - +
122B ILE* 1.3 66.4 + - - +
128B ILE* 4.3 11.0 - - + -
135B VAL* 3.8 18.4 - - + +
136B PRO* 3.2 25.5 - - - +
301B LEU* 3.9 4.4 - - - +
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B VAL* 4.8 3.6 - - + -
97B VAL 3.1 6.2 + - - +
98B ILE* 3.3 28.4 - - + -
99B VAL* 2.9 23.7 + - - +
121B VAL* 1.3 79.2 - - - +
123B SER* 1.3 71.9 + - - +
136B PRO* 3.4 18.8 - - + +
138B VAL* 3.7 22.7 - - + -
287B ALA* 4.5 10.8 - - + +
290B GLN* 3.6 32.1 - - + +
301B LEU* 4.0 21.5 - - + -
302B LYS 4.2 4.9 - - - +
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ILE* 5.0 0.2 - - - -
99B VAL* 3.1 11.7 - - - +
101B PRO* 4.4 0.2 - - - -
122B ILE* 1.3 81.2 - - - +
124B VAL* 1.3 61.3 + - - +
126B ARG 3.4 13.9 - - - -
127B ASN* 3.6 9.1 - - - -
128B ILE* 4.0 19.5 + - - -
135B VAL* 3.9 5.4 + - - +
136B PRO 3.0 8.1 + - - -
137B HIS* 2.7 34.2 + - - +
138B VAL* 2.9 25.1 + - - +
287B ALA* 5.2 0.2 - - - +
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL* 5.7 2.7 - - + -
44B PHE* 5.8 1.8 - - + -
55B MSE 4.5 13.2 - - - -
98B ILE* 3.8 25.1 - - + -
99B VAL 3.0 11.3 + - - +
100B ALA* 3.5 23.9 - - + +
123B SER* 1.3 75.1 - - - +
125B ASP* 1.3 61.6 + - + +
126B ARG 2.8 19.6 + - - +
137B HIS* 4.1 0.2 - - - -
138B VAL 3.2 9.4 - - - +
283B GLN* 4.0 34.3 - - + +
284B ILE* 4.2 17.5 - - + +
287B ALA* 4.6 5.4 - - + -
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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