Contacts of the strand formed by residues 125 - 129 (chain C) in PDB entry 4IJ3
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 SER 125 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123C PRO 5.0 1.6 + - - -
124C PRO* 1.3 71.9 - - - +
126C VAL* 1.3 60.8 + - - +
127C TYR* 3.5 32.8 + - - -
146C LEU 3.2 4.7 - - - +
147C VAL* 3.5 1.2 - - - -
148C LYS* 2.9 40.1 + - - +
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Residues in contact with VAL 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLU* 5.2 0.3 - - - +
124C PRO* 3.9 11.1 + - + +
125C SER* 1.3 75.9 - - - +
127C TYR* 1.3 68.9 + - - +
128C PRO* 4.2 0.2 - - - +
145C CYS* 4.0 6.3 - - + -
146C LEU 3.3 6.1 - - - +
147C VAL* 4.5 4.5 - - + -
200C CYS* 4.0 18.4 - - - -
202C VAL* 3.9 34.3 - - + -
211C VAL* 4.2 24.9 - - + -
213C LYS* 3.2 44.9 + - + +
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Residues in contact with TYR 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B SER* 3.4 24.2 - - - +
123B GLU* 4.1 13.5 - - + -
124B GLN* 3.5 56.4 - - + +
127B SER* 3.9 17.0 + - - -
125C SER* 3.5 33.1 + - - -
126C VAL* 1.3 81.5 - - - +
128C PRO* 1.3 66.0 - - - +
129C LEU* 5.5 2.0 - - + -
145C CYS* 3.5 4.7 - - - -
146C LEU* 2.9 56.5 + - + +
148C LYS* 4.6 10.2 - - + -
213C LYS* 4.6 0.4 - - - -
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Residues in contact with PRO 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B SER* 3.5 17.4 - - - -
123B GLU* 3.6 38.6 - - + +
127C TYR* 1.3 85.0 - - + +
129C LEU* 1.3 64.3 + - - +
130C ALA* 3.7 5.2 + - + +
144C GLY 4.0 0.2 - - - +
145C CYS* 4.7 0.4 - - - -
213C LYS* 3.9 22.8 - - + -
214C LYS 4.1 8.1 - - - +
215C ILE* 3.5 27.4 - - + -
216C VAL* 5.3 5.8 - - + +
218C ARG* 4.6 2.3 + - - -
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B PHE* 3.6 24.8 - - + -
119B PRO 4.6 8.7 - - - +
121B SER 5.7 2.0 - - - +
131B SER 5.7 1.1 - - - +
133B VAL* 4.0 33.0 - - + -
135B PHE* 3.9 24.0 - - + -
127C TYR* 4.6 2.5 - - + +
128C PRO* 1.3 77.4 - - - +
130C ALA* 1.3 60.0 + - - +
143C LEU* 3.5 9.0 - - - -
144C GLY* 2.7 52.2 + - - +
145C CYS* 3.8 18.2 - - - +
146C LEU* 4.1 11.7 - - + +
183C SER* 5.0 0.7 - - - -
215C ILE* 3.7 5.7 - - - +
218C ARG* 5.1 0.7 - - - +
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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