Contacts of the strand formed by residues 173 - 184 (chain A) in PDB entry 2VDY
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 LEU 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LEU* 6.0 0.7 - - + -
109A LEU* 3.9 33.7 - - + -
110A PHE 3.4 4.0 - - - -
111A LEU* 3.9 21.1 - - + -
115A LEU* 5.2 0.2 - - + -
171A ALA* 3.9 1.0 - - - +
172A ILE* 1.3 81.0 - - + +
174A VAL* 1.3 72.6 + - - +
175A LEU* 4.1 13.0 - - + +
312A ILE* 3.7 37.5 - - + -
318A LEU* 4.1 15.5 - - + -
344A LEU* 4.7 5.6 - - + +
345A GLU* 3.6 0.2 - - - -
346A ALA* 2.9 51.5 + - + +
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.6 2.5 - - - +
110A PHE* 2.8 44.7 + - + +
136A MET* 4.8 3.4 - - + -
141A TRP* 4.4 7.4 - - + -
148A ILE* 4.1 20.4 - - + -
164A PHE* 3.6 29.2 - - + -
171A ALA* 4.5 7.2 - - + +
173A LEU* 1.3 83.3 - - - +
175A LEU* 1.3 62.6 + - - +
176A VAL* 3.8 21.1 - - + -
343A PHE* 4.3 2.7 - - + -
344A LEU 3.3 7.6 - - - +
345A GLU* 4.1 20.9 - - + +
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ALA* 3.7 33.0 - - + +
54A MET* 3.8 30.5 - - + +
55A LEU* 4.0 41.3 - - + +
107A ASN* 5.9 0.4 - - - +
108A ALA 3.7 3.1 - - - -
109A LEU* 4.1 13.2 - - + -
121A PHE* 5.8 3.6 - - + -
173A LEU* 4.1 4.3 - - + +
174A VAL* 1.3 72.6 - - - +
176A VAL* 1.3 68.7 + - - +
177A ASN* 5.4 0.2 - - + -
312A ILE* 6.3 0.9 - - + -
342A MET* 3.9 1.5 - - + +
343A PHE* 3.2 6.4 - - - +
344A LEU* 2.8 54.0 + - + +
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ASN* 3.4 6.3 - - - +
108A ALA* 2.8 43.9 + - + +
110A PHE* 3.8 21.5 - - + -
148A ILE* 4.1 8.5 - - + -
151A TYR* 5.0 5.2 - - + -
152A VAL* 3.8 25.4 - - + -
163A LEU* 4.9 2.7 - - + -
174A VAL* 3.8 19.7 - - + -
175A LEU* 1.3 87.3 - - - +
177A ASN* 1.3 72.5 + - - +
178A TYR* 4.9 7.9 - - + +
342A MET 3.4 8.3 - - - +
343A PHE* 4.4 6.1 - - + -
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Residues in contact with ASN 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A SER* 2.7 39.0 + - - +
50A MET* 3.6 26.3 - - - +
51A ALA* 3.7 20.6 - - + -
105A MET* 4.3 5.7 - - - +
106A GLY 3.4 11.0 + - - -
107A ASN* 2.8 24.3 + - - +
175A LEU* 4.9 1.0 - - + +
176A VAL* 1.3 75.9 - - - +
178A TYR* 1.3 68.2 + - - +
341A ALA* 3.2 4.7 - - - +
342A MET* 2.8 35.3 + - + +
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Residues in contact with TYR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A THR* 4.1 14.4 + - + -
105A MET* 3.4 13.2 + - - +
106A GLY* 3.0 63.9 + - - +
107A ASN* 4.1 3.4 - - - -
132A GLU* 5.4 0.2 + - - -
151A TYR* 4.1 21.3 + + - -
152A VAL* 4.9 7.4 - - + -
155A LYS* 3.4 64.4 + - + +
156A THR* 3.9 16.8 - - + -
176A VAL* 5.0 5.8 - - + -
177A ASN* 1.3 80.8 + - - +
179A ILE* 1.3 63.9 + - - +
340A GLY 3.3 6.1 - - - +
341A ALA* 4.6 5.2 - - + -
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Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A SER* 3.4 29.8 - - - +
46A VAL* 4.1 18.4 - - + -
47A SER* 4.0 7.0 - - - -
94A PHE* 5.5 0.4 - - + -
103A MET* 5.3 8.7 - - + -
104A THR 3.5 10.3 - - - +
105A MET* 4.1 19.7 - - + -
156A THR* 3.9 4.5 - - - +
178A TYR* 1.3 75.2 - - - +
180A PHE* 1.3 69.1 + - - +
181A PHE* 5.4 1.8 - - + -
339A ALA* 3.2 5.4 - - - +
340A GLY* 2.7 58.2 + - - +
374A LEU* 4.8 9.9 - - + -
375A PHE* 4.1 23.1 - - + -
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Residues in contact with PHE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLU* 3.8 31.4 - - + -
103A MET* 3.4 6.8 - - - +
104A THR* 2.9 55.0 + - + +
156A THR* 3.3 37.7 - - + -
157A GLN* 3.9 23.3 - - + -
159A LYS* 3.7 26.0 - - + -
179A ILE* 1.3 76.8 - - - +
181A PHE* 1.3 66.4 - - - +
182A LYS* 4.1 26.7 - - + -
337A GLU* 5.5 4.5 - - + -
338A ALA 3.7 3.8 - - - -
339A ALA* 4.3 5.6 - - + -
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Residues in contact with PHE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 4.2 14.4 - - + -
102A GLU 3.7 5.2 - - - -
103A MET* 4.3 24.2 - - + +
179A ILE* 5.1 1.8 - - + -
180A PHE* 1.3 81.9 - - - +
182A LYS* 1.3 66.0 + - - +
183A GLY* 3.7 29.8 - - - -
235A TYR* 3.9 37.7 - + + -
239A GLY* 5.2 7.4 - - - -
336A THR* 4.5 7.4 - - + -
337A GLU* 3.4 3.8 - - - +
338A ALA* 2.7 52.6 + - + +
365A ILE* 4.4 11.2 - - + -
374A LEU* 5.0 8.5 - - + -
375A PHE* 3.7 28.7 - + + -
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Residues in contact with LYS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A THR 5.4 6.0 + - - -
100A SER* 4.1 5.0 - - - +
101A LEU* 3.7 8.3 - - - +
102A GLU* 2.8 61.0 + - + +
180A PHE* 4.1 15.9 - - + -
181A PHE* 1.3 76.3 - - - +
183A GLY* 1.3 61.8 + - - +
184A THR* 5.8 4.7 - - - +
336A THR 3.5 3.4 - - - +
337A GLU* 3.9 31.9 - - + +
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Residues in contact with GLY 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A SER 4.5 0.9 - - - -
101A LEU* 4.8 3.4 - - - -
181A PHE* 3.7 23.3 - - - -
182A LYS* 1.3 77.9 - - - +
184A THR* 1.3 63.6 + - - -
235A TYR* 3.8 13.7 - - - -
335A GLY* 3.3 2.8 - - - -
336A THR 2.9 32.3 + - - +
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Residues in contact with THR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A SER* 2.8 39.8 + - - +
182A LYS* 5.8 4.2 - - - +
183A GLY* 1.3 73.2 + - - -
185A TRP* 1.3 70.6 + - - +
188A PRO* 6.4 0.4 - - + -
235A TYR* 3.3 8.3 - - - +
236A VAL* 2.9 40.2 + - + +
334A GLU* 3.4 21.1 - - + +
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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