Contacts of the strand formed by residues 123 - 127 (chain E) in PDB entry 4WFH
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 123 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121E PRO 3.9 1.3 + - - -
122E PRO* 1.3 71.2 - - - +
124E VAL* 1.3 60.2 + - - +
125E TYR* 3.5 36.8 + - - -
144E LEU 3.5 1.6 - - - +
145E VAL* 3.4 3.6 - - - -
146E LYS* 2.8 41.1 + - - +
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Residues in contact with VAL 124 (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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122E PRO* 3.9 12.5 + - + +
123E SER* 1.3 76.7 - - - +
125E TYR* 1.3 70.9 + - - +
126E PRO* 4.4 0.2 - - - +
143E CYS* 4.3 2.7 - - - -
144E LEU 3.3 7.0 - - - +
145E VAL* 4.5 5.4 - - + -
198E CYS* 4.0 8.3 - - - -
200E VAL* 3.9 44.9 - - + -
209E VAL* 4.0 22.7 - - + -
211E LYS* 3.4 45.2 + - + +
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Residues in contact with TYR 125 (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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120D SER* 3.6 23.6 - - - +
122D GLU* 3.8 17.9 + - + -
123D GLN* 3.6 38.0 - - + +
126D SER* 3.5 18.9 + - - -
123E SER* 3.5 33.5 + - - -
124E VAL* 1.3 85.0 - - - +
126E PRO* 1.3 66.5 - - - +
127E LEU* 5.6 1.1 - - + -
143E CYS* 3.7 2.5 - - - -
144E LEU* 2.8 57.6 + - + +
146E LYS* 4.0 16.8 - - + -
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Residues in contact with PRO 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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118D PRO 5.3 0.7 - - - +
120D SER* 3.8 16.8 + - - -
122D GLU* 3.7 35.7 - - - +
125E TYR* 1.3 90.2 - - + +
127E LEU* 1.3 66.9 + - - +
128E ALA* 3.9 3.6 + - + +
142E GLY 3.9 0.9 - - - +
143E CYS* 4.6 2.7 - - - -
211E LYS* 4.2 13.8 - - + -
212E LYS 4.1 11.9 - - - +
213E ILE* 3.5 29.8 - - + -
214E VAL 5.3 1.6 - - - +
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Residues in contact with LEU 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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117D PHE* 3.3 34.0 - - + +
118D PRO 4.7 9.4 - - - +
119D PRO* 6.1 0.2 - - + -
120D SER 5.6 2.2 - - - +
130D SER 5.5 2.9 - - - +
132D VAL* 4.1 25.8 - - + -
134D PHE* 3.8 28.7 - - + -
125E TYR* 4.5 1.8 - - + +
126E PRO* 1.3 82.0 - - - +
128E ALA* 1.3 59.6 + - - +
141E LEU* 3.7 4.0 - - - -
142E GLY* 2.9 44.0 + - - +
143E CYS 4.0 3.4 - - - +
144E LEU* 4.0 27.6 - - + +
181E SER* 4.6 1.6 - - - -
213E ILE* 3.8 5.7 - - - +
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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