Contacts of the strand formed by residues 169 - 177 (chain I) 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 LYS 169 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I GLU* 4.5 11.0 + - - +
82I PRO* 3.4 31.5 - - - +
111I PRO* 4.0 19.2 - - + +
112I ASN 5.0 7.9 - - - +
113I ILE* 3.3 36.2 - - + +
160I VAL* 4.7 8.6 - - + +
161I LEU 3.2 9.0 - - - +
162I ASP* 3.8 29.4 + - + +
167I ASP 3.8 6.0 + - - +
168I PHE* 1.3 88.4 - - - +
170I SER* 1.3 64.3 + - - +
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Residues in contact with SER 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113I ILE* 4.6 3.4 - - - -
137I THR* 4.7 0.4 - - - -
138I ASP* 3.6 15.0 - - - +
159I THR 3.9 0.3 - - - +
160I VAL* 3.6 2.8 - - - +
161I LEU* 2.8 55.3 + - - +
168I PHE* 3.6 10.7 - - - -
169I LYS* 1.3 78.7 - - - +
171I ASN* 1.3 66.6 + - - +
172I SER* 4.7 0.9 + - - -
195J ARG* 3.3 29.9 + - - -
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Residues in contact with ASN 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111I PRO* 4.5 0.7 - - - +
113I ILE* 4.3 10.7 - - - +
137I THR* 3.2 13.3 + - - -
138I ASP* 3.2 13.2 + - - +
139I PHE* 3.2 45.4 + - + +
140I ASP 4.2 1.0 - - - -
141I SER* 3.5 27.5 + - - +
158I LYS* 4.1 19.5 + - + +
159I THR 3.3 7.1 - - - +
160I VAL* 3.3 26.6 - - - +
170I SER* 1.3 74.9 - - - +
172I SER* 1.3 67.3 + - - +
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Residues in contact with SER 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I LEU* 3.9 15.9 - - - -
136I PHE 3.3 11.4 - - - -
137I THR* 3.6 14.6 - - - -
139I PHE* 3.9 4.2 - - - -
158I LYS* 3.4 3.9 - - - +
159I THR* 3.1 25.1 + - - +
161I LEU* 5.4 6.8 - - - +
170I SER 4.7 1.9 + - - -
171I ASN* 1.3 78.8 - - - +
173I ALA* 1.3 57.1 + - - +
193J ARG* 2.8 42.4 + - - +
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Residues in contact with ALA 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I CYS 4.0 0.2 - - - +
135I LEU* 3.9 3.9 - - - +
136I PHE* 3.1 35.7 + - + +
139I PHE* 4.4 0.9 - - + -
145I VAL* 4.3 20.6 - - + -
156I THR* 3.7 26.0 - - - +
157I ASP 4.3 5.2 - - - +
158I LYS* 4.6 2.0 - - - -
172I SER* 1.3 73.9 - - - +
174I VAL* 1.3 66.5 + - - +
188I PHE* 4.4 13.9 - - + -
193J ARG* 3.7 1.6 - - - +
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Residues in contact with VAL 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I VAL* 4.1 20.4 - - + -
134I CYS 3.6 10.1 - - - +
135I LEU* 4.4 8.7 - - + -
155I ILE* 3.5 6.4 - - - +
156I THR* 3.1 36.1 + - + +
173I ALA* 1.3 78.8 - - - +
175I ALA* 1.3 63.6 + - - +
176I TRP* 4.0 17.9 - - + -
188I PHE* 4.4 2.2 - - - -
144J VAL* 4.5 17.5 - - + -
146J LEU* 4.9 0.7 - - + -
191J SER* 3.9 23.1 - - - +
193J ARG* 4.0 25.1 - - + +
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Residues in contact with ALA 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I VAL* 3.5 1.9 - - - +
134I CYS* 2.9 37.9 + - + +
153I VAL* 5.6 0.7 - - + -
154I TYR 3.3 9.2 - - - +
155I ILE* 4.3 10.8 - - + -
174I VAL* 1.3 74.8 - - - +
176I TRP* 1.3 65.5 + - - +
182I PHE* 4.4 5.6 - - + -
187I ALA* 4.1 21.3 - - + -
188I PHE* 3.8 21.5 - - + -
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Residues in contact with TRP 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I LYS* 6.5 1.3 - - - -
132I SER 4.2 5.2 - - - +
133I VAL* 3.7 18.2 - - + -
153I VAL* 4.0 0.9 - - - +
154I TYR* 3.0 68.8 + + + -
156I THR* 3.7 23.6 - - + -
174I VAL* 4.0 10.8 - - + -
175I ALA* 1.3 80.8 - - - +
177I SER* 1.3 66.1 + - - +
182I PHE* 4.2 8.2 - - - -
146J LEU* 3.7 31.4 - - + +
148J THR* 4.7 6.7 - - + +
177J LEU* 3.6 21.1 - - + -
189J SER* 3.6 31.7 + - - -
190J LEU 5.0 4.0 - - - -
191J SER* 4.3 13.9 - - - -
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Residues in contact with SER 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131I LYS* 5.0 6.1 - - - +
132I SER 4.5 11.5 + - - +
152I ASP 2.5 26.4 + - - -
153I VAL* 3.8 5.0 - - - +
154I TYR* 5.0 2.9 - - - -
176I TRP* 1.3 83.3 - - - +
178I ASN* 1.3 69.5 + - - +
179I LYS* 3.5 17.0 + - - +
182I PHE* 3.7 41.1 - - - +
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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