Contacts of the strand formed by residues 125 - 129 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E HIS 3.9 1.0 + - - +
33E VAL* 3.7 8.0 - - + +
34E CYS* 3.1 23.2 + - - +
123E PHE* 3.4 0.8 - - - +
124E THR* 1.3 99.7 - - + +
126E VAL* 1.3 76.3 + - - +
127E VAL* 3.9 14.5 + - + -
148E ILE* 4.7 0.7 - - - -
149E PRO* 3.6 20.4 - - + +
151E LEU* 4.9 4.0 - - + -
505E VAL* 4.3 16.6 - - + -
508E ILE* 3.6 41.5 - - + -
509E ILE* 4.5 6.1 - - + -
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Residues in contact with VAL 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E CYS* 3.4 22.9 - - + +
36E ILE* 4.0 22.4 - - + -
120E PHE* 3.8 25.8 - - + -
123E PHE* 4.1 8.1 - - + -
125E VAL* 1.3 78.5 - - - +
127E VAL* 1.3 64.0 + - - +
139E LEU* 4.7 0.4 - - + -
143E LEU* 3.9 16.8 - - + -
148E ILE* 3.9 18.2 - - + -
149E PRO 2.9 9.9 + - - +
150E LEU* 3.4 16.0 - - + +
151E LEU 2.9 25.1 + - - -
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Residues in contact with VAL 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E VAL* 4.3 14.4 - - + -
34E CYS 2.7 12.1 + - - +
35E LEU* 3.3 13.2 - - + +
36E ILE 2.7 29.4 + - - -
45E ILE* 3.9 35.2 - - + -
49E LEU* 5.5 0.4 - - + -
125E VAL* 4.1 9.0 - - + -
126E VAL* 1.3 76.0 - - - +
128E ALA* 1.3 54.5 + - - +
129E THR* 4.1 7.6 - - + -
151E LEU* 3.4 14.4 - - + +
153E CYS* 4.5 4.5 - - - -
505E VAL* 3.6 30.3 - - + -
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Residues in contact with ALA 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E ILE* 3.6 18.6 - - + -
126E VAL 3.9 1.8 + - - -
127E VAL* 1.3 73.6 - - - +
129E THR* 1.3 62.4 + - - +
131E LEU* 3.4 30.1 - - + -
139E LEU* 4.1 11.2 - - + -
150E LEU* 4.3 6.3 - - + -
151E LEU 2.9 9.2 + - - +
152E ILE* 3.3 7.8 - - + +
153E CYS 2.8 27.3 + - - +
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Residues in contact with THR 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E LEU* 3.9 8.7 - - + -
36E ILE* 4.2 0.6 - - - +
37E ASN* 2.5 48.7 + - - +
39E THR* 4.0 2.8 + - - -
41E THR* 4.5 3.8 - - + -
42E GLY* 3.6 31.1 + - - +
45E ILE* 3.8 19.1 - - + -
127E VAL* 4.0 3.7 + - + -
128E ALA* 1.3 81.6 - - - +
130E GLN* 1.3 76.8 + - - +
131E LEU* 3.6 3.7 - - - +
153E CYS* 3.2 10.1 - - + -
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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