Contacts of the strand formed by residues 120 - 124 (chain F) in PDB entry 4MXV
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 120 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117F LYS* 4.1 12.6 + - - -
118F GLY 4.1 0.2 + - - -
119F PRO* 1.3 73.7 + - - +
121F VAL* 1.3 61.6 + - - +
122F PHE* 3.6 27.7 + - - -
141F LEU 3.4 1.6 - - - +
142F VAL* 3.7 0.9 - - - -
143F LYS* 2.9 37.4 + - - +
144F ASP* 5.3 1.8 + - - +
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Residues in contact with VAL 121 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123E GLU* 3.9 1.6 - - - +
119F PRO* 4.3 6.0 + - + +
120F SER* 1.3 77.8 - - - +
122F PHE* 1.3 69.8 + - - +
140F CYS* 4.2 7.9 - - + -
141F LEU 3.3 6.7 - - - +
142F VAL* 4.3 7.4 - - + -
196F CYS* 4.1 15.7 - - - -
198F VAL* 3.7 32.1 - - + -
207F VAL* 3.7 24.8 - - + +
209F LYS* 3.3 47.0 + - + -
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Residues in contact with PHE 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E SER* 3.5 25.1 - - - +
123E GLU* 3.7 22.2 - - + -
124E GLN* 3.4 45.8 - - + +
127E SER* 4.4 10.5 - - - -
120F SER* 3.6 32.5 - - - -
121F VAL* 1.3 83.7 - - - +
123F PRO* 1.3 66.3 - - - +
140F CYS* 3.4 4.3 - - - +
141F LEU* 2.6 51.5 + - + +
143F LYS* 4.0 19.3 - - + -
209F LYS* 4.8 1.1 - - - -
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Residues in contact with PRO 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E PRO 4.8 2.8 - - - +
121E SER* 3.9 29.1 + - - -
123E GLU* 3.8 19.1 - - + +
122F PHE* 1.3 88.2 - - + +
124F LEU* 1.3 65.8 + - - +
125F ALA* 3.6 11.6 + - + +
139F GLY 3.8 4.9 - - - +
140F CYS* 4.7 0.4 - - - -
209F LYS* 4.3 13.2 - - + -
210F LYS 4.9 2.5 - - - +
211F VAL* 4.3 23.8 - - + -
212F GLU 5.4 2.2 - - - +
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Residues in contact with LEU 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E PHE* 3.6 28.7 - - + -
119E PRO 5.0 5.2 - - - +
131E SER 5.9 0.9 - - - +
133E VAL* 4.0 40.2 - - + -
122F PHE* 6.1 0.2 - - + -
123F PRO* 1.3 77.2 - - - +
125F ALA* 1.3 64.8 + - - +
138F LEU* 3.5 4.9 - - - -
139F GLY 2.7 47.2 + - - +
140F CYS 4.0 9.9 - - - +
141F LEU* 4.1 17.3 - - + +
179F SER* 4.3 9.4 - - - -
181F VAL* 4.2 18.6 - - + -
211F VAL* 3.6 5.6 - - - +
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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