Contacts of the strand formed by residues 120 - 124 (chain L) in PDB entry 6VEN
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 120 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95L HIS* 4.9 0.2 - - - -
112L PHE 5.3 0.4 - - - -
113L THR 3.2 21.8 - - - +
119L SER* 1.3 78.1 - - - +
121L LYS* 1.3 78.3 + - - +
122L ILE* 4.7 10.5 - - + -
133L THR* 3.4 2.9 + - - -
134L ILE* 2.9 45.2 + - + +
137L HIS* 5.1 2.7 - - + -
141L VAL* 4.0 11.9 - - + -
144L VAL* 3.7 19.3 - - + -
154L LEU* 4.8 9.9 - - + -
156L SER* 3.5 34.5 - - - +
166L PHE* 4.3 16.4 - - + -
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Residues in contact with LYS 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L GLY* 4.0 22.7 - - - -
95L HIS* 3.4 22.4 + - + +
111L LEU 3.7 1.0 - - - +
112L PHE* 3.6 3.6 - - - -
113L THR* 2.9 49.1 + - - +
117L ASP* 5.6 1.9 + - - -
119L SER* 4.4 10.0 + - - +
120L ILE* 1.3 77.6 - - - +
122L ILE* 1.3 64.4 + - - +
123L TRP* 3.5 25.9 - - + +
130L LEU* 3.7 24.2 - - + +
132L LYS 3.4 5.6 - - - +
133L THR* 3.1 24.2 + - - +
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Residues in contact with ILE 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110L LEU* 4.0 26.9 - - + -
111L LEU 3.4 5.6 - - - +
112L PHE* 3.4 40.8 - - + -
120L ILE* 4.7 4.7 - - + -
121L LYS* 1.3 77.2 - - - +
123L TRP* 1.3 54.8 + - - +
130L LEU* 3.3 2.9 - - - +
131L MET* 2.7 34.3 + - + +
132L LYS* 2.9 39.3 + - + +
134L ILE* 4.3 24.0 - - + -
154L LEU* 4.5 8.1 - - + -
167L ASP 5.6 2.5 - - - +
168L ALA* 4.8 7.6 - - - +
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Residues in contact with TRP 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L VAL* 4.5 1.0 - - + +
92L PHE* 3.8 48.2 - + + -
93L ILE 4.6 0.7 - - - -
94L GLY* 3.4 35.0 - - - -
95L HIS* 3.8 16.8 - + - -
110L LEU* 3.4 10.0 - - - +
111L LEU* 2.9 44.9 + - + +
113L THR* 2.6 46.4 + - + +
121L LYS* 3.5 31.1 - - + +
122L ILE* 1.3 74.3 - - - +
124L ASP* 1.3 59.5 + - - +
125L THR 3.9 0.2 - - - -
128L GLY 5.6 0.4 - - - -
129L SER 3.7 4.0 - - - +
130L LEU* 3.5 41.3 - - + -
131L MET* 4.3 0.2 - - - -
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Residues in contact with ASP 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92L PHE* 3.8 3.4 - - - -
109L ASN* 3.6 11.6 - - - +
110L LEU* 3.7 4.9 - - + -
123L TRP* 1.3 72.5 - - - +
125L THR* 1.3 62.3 + - - +
126L LEU* 3.5 11.0 + - - +
127L ASN* 3.1 28.1 + - + +
128L GLY* 2.9 30.1 + - - -
129L SER* 2.7 21.6 + - - +
131L MET* 3.7 19.8 - - + +
57M THR* 4.1 14.4 - - - +
59M ARG* 3.1 19.1 + - - +
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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