Contacts of the strand formed by residues 129 - 139 (chain L) in PDB entry 2VDP
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 GLY 129 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149H LYS* 6.2 1.1 - - - -
124L GLN* 3.1 34.3 + - - +
125L LEU* 3.6 8.5 - - - +
127L SER* 3.6 5.2 + - - -
128L GLY* 1.3 80.8 - - - +
130L ALA* 1.3 63.2 + - - +
180L THR* 5.9 2.5 - - - -
181L LEU 4.2 2.5 - - - -
182L THR* 5.3 1.1 - - - -
183L LYS* 4.0 2.9 - - - +
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Residues in contact with ALA 130 (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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120L PRO* 4.0 11.7 - - + -
124L GLN* 3.7 5.4 - - - +
125L LEU* 4.0 6.1 - - + -
129L GLY* 1.3 76.6 - - - +
131L SER* 1.3 60.9 + - - +
180L THR* 3.5 3.6 - - - +
181L LEU* 2.9 47.2 + - + +
183L LYS* 4.0 4.0 - - - -
186L TYR* 3.7 34.5 - - + -
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Residues in contact with SER 131 (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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130H LEU* 5.7 1.9 - - - +
147H LEU* 3.8 19.5 - - - +
149H LYS* 3.9 7.6 - - - +
119L PRO 4.0 1.0 - - - -
120L PRO* 3.4 24.6 - - - +
124L GLN* 2.8 31.6 + - - +
130L ALA* 1.3 71.0 - - - +
132L VAL* 1.3 62.6 + - - +
133L VAL* 4.0 3.8 + - - +
178L THR* 3.8 11.7 - - - -
179L LEU 3.2 4.5 - - - -
180L THR* 3.0 23.6 + - - +
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Residues in contact with VAL 132 (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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117L ILE* 4.0 5.4 - - + -
118L PHE 3.5 16.4 - - - +
120L PRO* 4.1 14.6 - - + -
131L SER* 1.3 75.2 - - - +
133L VAL* 1.3 59.0 + - - +
148L TRP* 3.3 33.6 - - + -
178L THR* 3.4 0.6 - - - -
179L LEU* 2.8 45.5 + - + +
181L LEU* 4.7 6.1 - - + -
186L TYR* 4.2 17.0 - - + -
192L TYR* 4.3 15.5 - - + -
209L PHE* 3.7 21.1 - - + -
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Residues in contact with VAL 133 (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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130H LEU* 3.8 28.7 - - + -
147H LEU* 3.9 24.7 - - + -
184H SER* 5.2 2.0 - - - -
117L ILE* 3.6 2.9 - - - +
118L PHE* 2.9 38.3 + - + +
131L SER 4.0 3.6 + - - +
132L VAL* 1.3 75.9 - - - +
134L CYS* 1.3 66.2 + - - +
135L PHE* 3.8 37.2 - - + -
148L TRP* 4.1 0.7 - - - -
176L SER* 4.4 3.4 - - - +
177L SER 3.4 7.0 - - - +
178L THR* 3.8 18.6 - - + +
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Residues in contact with CYS 134 (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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115L VAL* 3.6 15.9 - - - -
116L SER 3.3 16.2 - - - -
117L ILE* 4.4 2.2 - - - -
133L VAL* 1.3 77.0 - - - +
135L PHE* 1.3 62.9 + - - +
136L LEU* 3.5 8.8 - - + +
148L TRP* 3.7 17.0 - - + -
176L SER* 3.5 1.6 - - - -
177L SER* 2.7 38.7 + - - +
194L CYS* 2.0 49.8 - - - -
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Residues in contact with PHE 135 (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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130H LEU* 4.4 5.4 - - + -
143H THR* 4.6 1.6 - - + -
144H LEU 4.5 0.2 - - - -
145H GLY* 4.0 10.8 - - - -
172H PHE* 3.5 34.8 - + - -
184H SER* 3.7 12.3 - - - -
185H SER 3.4 22.4 - - - -
186H SER* 3.6 18.6 - - - -
114L THR 3.2 5.7 - - - +
115L VAL* 3.3 1.4 - - - -
116L SER* 2.9 37.3 + - - +
118L PHE* 3.5 31.9 - + - -
133L VAL* 3.8 18.2 - - + -
134L CYS* 1.3 72.4 - - - +
136L LEU* 1.3 61.1 + - - +
137L ASN* 3.7 18.8 - - - +
175L MET 3.6 1.1 - - - -
176L SER* 3.6 19.5 - - - -
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Residues in contact with LEU 136 (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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113L PRO* 4.2 12.3 - - + -
114L THR 4.1 2.7 - - - -
115L VAL* 4.1 13.5 - - + +
134L CYS* 3.5 29.2 - - + +
135L PHE* 1.3 77.5 - - - +
137L ASN* 1.3 59.7 + - - +
139L PHE* 3.3 10.3 - - + -
144L ILE* 3.6 21.8 - - + -
146L VAL* 4.4 21.1 - - + -
175L MET* 2.7 52.6 + - + +
177L SER* 4.9 4.0 - - - -
194L CYS* 4.5 3.1 - - - -
196L ALA* 3.3 30.3 - - + -
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Residues in contact with ASN 137 (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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143H THR* 4.7 9.9 + - - +
170H HIS* 3.7 10.6 - - - -
172H PHE* 3.6 14.6 - - - -
186H SER* 3.1 23.6 + - - -
188H THR* 4.8 5.9 + - - -
113L PRO* 3.4 1.6 - - - +
114L THR* 3.0 43.9 + - - +
116L SER* 5.8 0.4 + - - -
135L PHE* 3.7 17.4 - - - +
136L LEU* 1.3 77.7 - - - +
138L ASN* 1.3 82.9 + - - +
139L PHE* 3.5 2.7 - - - -
174L SER* 3.3 17.4 + - - +
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Residues in contact with ASN 138 (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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170H HIS* 2.6 34.0 + - - -
111L ALA* 3.8 10.6 - - - +
112L ALA 3.6 10.6 - - - +
114L THR* 5.3 3.3 + - - +
137L ASN* 1.3 81.0 - - - +
139L PHE* 1.3 57.4 + - - +
167L ASP* 5.1 0.8 + - - -
170L ASP* 3.0 27.6 + - - +
172L THR* 3.2 20.9 + - + +
173L TYR 3.1 5.0 + - - -
174L SER* 2.9 13.5 + - - -
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Residues in contact with PHE 139 (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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111L ALA* 3.2 14.4 - - - +
113L PRO* 3.7 30.5 - - + -
136L LEU 3.3 25.4 - - - -
137L ASN 4.2 0.2 - - - -
138L ASN* 1.3 74.8 - - - +
140L TYR* 1.3 62.9 + - - +
141L PRO 3.4 14.8 - - - -
142L LYS 3.4 24.2 - - - -
144L ILE* 3.7 31.2 - - + -
163L TRP* 5.4 2.7 - + - -
172L THR* 3.7 2.6 - - - -
173L TYR* 2.8 64.8 + - + +
174L SER* 3.7 8.5 - - - -
175L MET* 3.7 6.7 - - + -
198L HIS* 3.8 8.1 - + - +
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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