Contacts of the strand formed by residues 109 - 118 (chain F) in PDB entry 2VLR
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 PHE 109 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101F CYS* 4.9 0.7 - - + -
102F ASP 3.9 6.1 - - - -
103F VAL* 4.2 1.6 - - - +
107F TRP 4.3 0.2 + - - -
108F ARG* 1.3 75.2 - - - +
110F LEU* 1.3 73.1 + - - +
111F ARG* 3.6 33.4 - - - -
112F GLY* 3.7 6.1 - - - -
130F LEU* 4.0 11.0 - - + -
160F LEU 3.8 26.0 - - - -
161F GLU* 3.8 40.8 - - + +
165F VAL* 3.8 25.4 - - + +
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Residues in contact with LEU 110 (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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2F SER* 4.3 10.5 - - - +
102F ASP* 3.0 22.4 + - + +
103F VAL* 3.5 26.2 - - - +
104F GLY* 3.8 12.8 - - - +
106F ASP* 6.1 0.2 - - - +
108F ARG 3.4 1.5 + - - +
109F PHE* 1.3 85.8 - - - +
111F ARG* 1.3 65.3 + - + +
128F GLU* 5.3 2.6 - - - +
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Residues in contact with ARG 111 (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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101F CYS* 3.3 2.3 - - - -
102F ASP* 2.7 45.7 + - + +
109F PHE* 3.6 14.9 - - - -
110F LEU* 1.3 83.1 - - + +
112F GLY* 1.3 66.1 + - - +
113F TYR* 3.6 42.9 + - + +
128F GLU* 3.5 50.1 + - + +
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Residues in contact with GLY 112 (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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100F GLY 3.5 8.7 - - - -
101F CYS* 4.4 0.7 - - - -
109F PHE* 3.7 13.7 - - - -
111F ARG* 1.3 82.3 + - - +
113F TYR* 1.3 68.4 + - - -
126F LEU 5.4 1.7 - - - +
127F LYS 5.3 0.7 - - - +
128F GLU* 5.2 5.6 + - - +
130F LEU* 3.7 26.2 - - - +
160F LEU* 4.3 8.3 - - - -
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Residues in contact with TYR 113 (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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6F ARG* 3.4 40.4 + - - -
98F MET* 4.0 32.3 - - + -
99F TYR* 3.5 4.6 - - - +
100F GLY 3.0 27.9 + - - +
102F ASP* 3.3 20.3 + - - -
111F ARG* 3.6 51.4 + - + -
112F GLY* 1.3 75.8 - - - -
114F HIS* 1.4 64.1 + - - +
115F GLN* 4.6 13.7 - - - +
126F LEU* 5.3 4.3 - - - -
130F LEU* 5.3 0.7 - - - -
160F LEU* 3.5 11.4 - - - +
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Residues in contact with HIS 114 (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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97F ARG* 3.1 31.7 + - - -
98F MET 3.5 8.1 - - - -
99F TYR* 4.0 20.6 - + + -
113F TYR* 1.4 75.7 - - - +
115F GLN* 1.4 62.7 + - - +
116F TYR* 3.7 25.3 - + - -
124F ILE 4.5 0.2 - - - +
125F ALA* 3.8 0.7 - - - -
126F LEU* 3.0 45.2 + - + +
133F TRP* 3.8 20.0 - + - -
147F TRP* 4.4 1.6 - + - -
156F LEU* 3.8 28.5 - - + -
160F LEU* 4.7 4.7 - - + -
7H PHE* 3.9 12.5 - + - -
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Residues in contact with GLN 115 (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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97F ARG* 3.5 3.9 - - - +
98F MET* 3.1 61.5 + - + +
113F TYR* 4.6 16.4 - - - +
114F HIS* 1.4 78.5 + - - +
116F TYR* 1.3 65.3 + - - +
124F ILE 3.4 4.9 - - - +
125F ALA* 3.7 26.7 - - + +
126F LEU 4.8 5.5 + - - -
58G LYS 5.4 4.0 - - - +
60G TRP* 3.4 26.4 - - + -
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Residues in contact with TYR 116 (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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74F HIS* 4.1 17.1 + + - -
77F ASP* 4.8 0.7 + - - -
95F VAL* 4.2 10.1 - - + -
96F GLN 3.3 12.8 - - - -
97F ARG* 3.1 43.0 + - + -
114F HIS* 3.7 18.2 - + - -
115F GLN* 1.3 81.1 - - - +
117F ALA* 1.3 53.9 + - - +
122F ASP* 3.8 1.0 - - - -
123F TYR* 2.8 40.6 + - + +
124F ILE* 2.8 33.7 + - + +
133F TRP* 6.3 0.2 - + - -
147F TRP* 3.6 25.0 - + - -
60G TRP* 3.8 10.3 - - - -
7H PHE* 4.2 10.4 + - - -
9H LEU* 4.1 27.5 - - + +
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Residues in contact with ALA 117 (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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95F VAL* 3.4 11.2 - - - +
96F GLN* 2.9 43.6 + - + +
116F TYR* 1.3 74.1 - - - +
118F TYR* 1.3 59.0 + - - +
120F GLY 4.6 0.7 - - - -
121F LYS 3.3 20.4 - - - +
123F TYR* 4.1 3.4 - - - +
60G TRP* 3.5 37.6 - - + -
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Residues in contact with TYR 118 (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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78F LEU* 4.8 5.7 + - + -
81F LEU* 3.4 39.7 - - + +
82F ARG* 4.1 4.7 + - - +
85F TYR* 3.6 40.4 - + - +
87F GLN* 2.8 27.3 + - - -
93F HIS* 3.4 26.0 - - + +
94F THR 3.3 17.3 - - - -
95F VAL* 4.0 8.7 - - + -
117F ALA* 1.3 73.2 - - - +
119F ASP* 1.3 86.2 + - + +
120F GLY 3.2 2.6 + - - -
121F LYS* 3.1 26.2 + - - +
123F TYR* 4.2 17.3 - - + +
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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