Contacts of the strand formed by residues 123 - 127 (chain B) in PDB entry 5EWL
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 ILE 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B ILE* 4.5 6.3 - - + -
97B VAL* 3.3 22.9 - - + +
99B PHE* 4.4 7.2 - - + -
112B LEU* 3.6 46.2 - - + +
115B ILE* 4.0 17.7 - - + -
116B SER* 3.7 18.8 - - - +
121B THR* 3.4 9.6 + - - +
122B PRO* 1.3 78.8 - - - +
124B LEU* 1.3 68.6 + - - +
142B MET 3.1 7.4 + - - +
143B PHE* 3.3 24.5 - - + -
144B PHE 3.0 24.9 + - - -
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Residues in contact with LEU 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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97B VAL 2.8 16.0 + - - +
98B VAL* 4.2 2.5 - - + -
99B PHE* 2.7 33.4 + - - +
122B PRO* 5.5 0.9 - - + -
123B ILE* 1.3 78.4 - - - +
125B GLY* 1.3 58.4 + - - +
126B ILE* 3.3 14.1 + - + +
144B PHE* 3.1 39.0 - - + +
146B PHE* 4.7 4.0 - - + -
296B GLY* 3.3 38.4 - - - +
299B ILE* 4.2 17.3 - - + -
300B ILE* 3.9 19.5 - - + -
339B LEU* 5.1 4.7 - - + -
351B PHE* 4.2 13.2 - - + -
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Residues in contact with GLY 125 (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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99B PHE* 3.6 6.5 - - - -
124B LEU* 1.3 67.5 - - - +
126B ILE* 1.3 55.0 + - - -
127B HIS 3.5 3.1 - - - -
130B SER* 3.6 28.0 - - - -
131B SER* 3.5 8.0 - - - -
143B PHE* 3.7 9.9 - - - -
144B PHE 2.8 12.4 + - - -
145B GLN* 3.3 3.2 - - - -
146B PHE* 2.8 31.1 + - - -
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Residues in contact with ILE 126 (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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98B VAL* 3.7 19.5 - - + -
99B PHE 2.9 19.9 + - - +
100B ALA* 3.5 18.2 - - + -
124B LEU* 3.6 19.5 - - + +
125B GLY* 1.3 73.5 - - - -
127B HIS* 1.4 53.6 + - - +
131B SER* 4.2 1.3 - - - -
146B PHE* 3.7 43.1 - - + +
289B LEU* 3.8 6.7 - - + -
292B ARG* 2.7 58.1 + - + +
293B VAL* 3.7 27.6 - - + +
296B GLY* 4.8 0.9 - - - -
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Residues in contact with HIS 127 (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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100B ALA* 4.2 4.3 - - + -
101B ASP 2.9 41.6 + - - -
102B ASP* 4.9 5.6 - - - +
125B GLY 3.5 2.6 - - - -
126B ILE* 1.4 82.9 - - - +
128B GLY* 1.3 68.6 + - - +
130B SER* 2.9 17.8 + - - -
131B SER* 3.8 6.9 - - - -
284B GLU* 3.9 33.3 - - + +
289B LEU* 4.1 31.4 - - + -
292B ARG* 3.8 18.4 + - - +
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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