Contacts of the strand formed by residues 125 - 129 (chain G) in PDB entry 1R4N
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 125 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32G HIS 3.9 1.3 + - - +
33G VAL* 3.7 7.9 - - + +
34G CYS* 3.1 23.0 + - - +
123G PHE* 3.4 1.2 - - - +
124G THR* 1.3 101.6 - - + +
126G VAL* 1.3 77.0 + - - +
127G VAL* 4.0 14.4 + - + -
148G ILE* 4.7 0.4 - - - -
149G PRO* 3.6 19.5 - - + +
151G LEU* 5.0 3.8 - - + -
505G VAL* 4.3 17.3 - - + +
508G ILE* 3.5 41.7 - - + -
509G ILE* 4.5 5.6 - - + -
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Residues in contact with VAL 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G CYS* 3.4 24.5 - - + +
36G ILE* 4.0 22.2 - - + -
120G PHE* 3.8 25.8 - - + -
123G PHE* 4.1 7.9 - - + -
125G VAL* 1.3 76.8 - - - +
127G VAL* 1.3 64.1 + - - +
139G LEU* 4.7 0.4 - - + -
143G LEU* 3.9 16.6 - - + -
148G ILE* 3.9 17.9 - - + +
149G PRO 2.9 9.2 + - - +
150G LEU* 3.4 15.3 - - + +
151G LEU* 2.9 25.5 + - - -
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Residues in contact with VAL 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G VAL* 4.3 14.6 - - + -
34G CYS 2.6 11.3 + - - +
35G LEU* 3.3 13.6 - - + +
36G ILE 2.7 30.3 + - - -
45G ILE* 4.0 35.2 - - + -
49G LEU* 5.5 0.2 - - + -
125G VAL* 4.1 9.6 - - + -
126G VAL* 1.3 74.6 - - - +
128G ALA* 1.3 54.3 + - - +
129G THR* 4.1 7.9 - - + -
151G LEU* 3.4 13.9 - - + +
153G CYS* 4.6 5.2 - - - -
505G VAL* 3.7 29.6 - - + -
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Residues in contact with ALA 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G ILE* 3.6 18.8 - - + -
126G VAL 3.9 2.0 + - - -
127G VAL* 1.3 73.2 - - - +
129G THR* 1.3 57.1 + - - +
131G LEU* 3.4 30.1 - - + -
139G LEU* 4.0 11.7 - - + -
150G LEU* 4.2 6.5 - - + -
151G LEU 2.9 8.8 + - - +
152G ILE* 3.3 8.2 - - + +
153G CYS 2.7 31.9 + - - +
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Residues in contact with THR 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G LEU* 3.9 9.0 - - + -
36G ILE* 4.2 4.9 - - - +
37G ASN* 2.4 45.4 + - - +
39G THR* 4.0 2.6 + - - -
41G THR* 4.5 3.4 - - + -
42G GLY* 3.6 29.6 + - - +
45G ILE* 3.8 20.6 - - + -
127G VAL* 4.0 3.5 + - + -
128G ALA* 1.3 80.5 - - - +
130G GLN* 1.3 76.1 + - - +
131G LEU* 3.6 4.2 - - - +
152G ILE* 6.2 0.2 - - - -
153G CYS* 3.2 10.3 - - + -
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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