Contacts of the strand formed by residues 127 - 134 (chain B) in PDB entry 1VEW
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 127 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ARG* 3.9 6.0 - - - +
125B GLY 3.9 1.6 + - - -
126B SER* 1.3 77.2 - - - +
128B TRP* 1.3 61.6 + - - -
143B THR 3.2 12.8 - - - -
145B ASN 3.7 11.2 - - - -
168B VAL* 2.8 36.8 + - - +
169B TRP* 3.3 16.1 - - - +
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Residues in contact with TRP 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ASN* 3.5 43.4 - - + +
81B HIS* 3.7 18.4 - + - -
83B LEU* 6.1 0.9 - - + -
84B PHE* 3.8 27.6 - + + -
123B ARG* 4.5 1.4 + - - +
127B GLY* 1.3 75.1 - - - -
129B ALA* 1.3 58.8 + - - +
130B TRP* 3.5 37.6 + + + +
142B SER* 3.2 7.3 - - - -
143B THR* 2.9 35.4 + - - +
145B ASN 3.3 21.3 + - - -
146B GLN* 3.0 18.8 + - - -
147B ASP 4.6 0.2 - - - -
165B GLY 4.4 1.8 - - - -
166B LEU 3.3 15.9 - - - -
167B ASP* 3.5 54.3 + - + -
168B VAL* 4.0 5.1 - - - +
169B TRP* 4.1 0.4 - - - +
207B OH 4.0 0.4 + - - -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE* 3.7 18.6 - - + +
119B ALA* 4.4 7.0 - - + +
120B ALA* 3.7 39.7 - - + +
128B TRP* 1.3 73.7 - - - +
130B TRP* 1.3 61.7 + - - +
141B VAL 3.6 6.3 - - - +
142B SER* 4.2 2.0 - - - -
165B GLY* 3.2 3.3 - - - -
166B LEU* 2.8 35.4 + - + +
168B VAL* 4.8 1.5 - - + +
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Residues in contact with TRP 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASN* 3.3 35.4 - - + -
83B LEU* 4.3 21.1 - - + -
116B PHE* 3.8 6.9 - - - -
128B TRP* 3.5 38.4 - + + +
129B ALA* 1.3 77.0 - - - +
131B LEU* 1.3 60.4 + - - +
132B VAL* 3.8 17.7 + - + -
139B ALA 3.7 0.3 - - - +
140B VAL* 3.3 8.8 - - - +
141B VAL* 2.7 48.5 + - + +
142B SER* 4.1 4.7 - - - -
143B THR* 3.0 22.2 + - + -
147B ASP 4.0 7.0 - - - -
148B SER* 4.8 1.3 - - - -
149B PRO* 3.6 26.6 - - + +
162B PRO* 4.0 20.4 - - + -
164B MET 3.5 8.7 - - - -
165B GLY* 3.7 23.6 - - - -
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 5.0 3.4 - - + -
102B ILE* 4.6 15.3 - - + -
106B PHE* 4.2 6.1 - - + -
112B PHE* 3.8 28.0 - - + -
116B PHE* 4.0 2.1 - - + -
130B TRP* 1.3 71.7 - - - +
132B VAL* 1.3 60.2 + - - +
138B LEU* 4.2 20.9 - - + -
139B ALA 3.5 26.7 - - - +
140B VAL* 4.4 1.3 - - + +
162B PRO 3.8 0.5 - - - -
163B ILE* 2.8 46.5 + - + +
164B MET* 2.9 43.6 + - + +
194B TRP* 5.4 2.2 - - + -
197B ALA* 6.3 0.2 - - + -
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B TRP* 3.8 20.2 - - + -
131B LEU* 1.3 78.4 - - - +
133B LEU* 1.3 59.8 + - - +
134B LYS* 4.1 13.5 - - + -
138B LEU* 3.3 9.7 - - - +
139B ALA* 2.8 55.5 + - + +
141B VAL* 3.9 18.2 - - + -
149B PRO* 3.9 20.2 - - + -
159B SER 3.7 16.2 - - - +
160B GLY 4.1 4.3 - - - -
161B PHE 3.2 12.8 - - - +
162B PRO* 4.1 4.3 - - + -
163B ILE* 4.4 1.1 - - - -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ARG* 5.8 0.2 - - - +
132B VAL* 1.3 72.7 - - - +
134B LYS* 1.3 59.4 + - - +
135B GLY 3.5 18.4 + - - +
136B ASP* 3.7 22.9 - - - +
137B LYS 3.5 19.3 - - - +
138B LEU* 4.0 11.7 - - + -
160B GLY* 3.6 0.7 - - - -
161B PHE* 2.8 40.0 + - + +
163B ILE* 4.2 14.4 - - + -
201B PHE* 4.5 19.3 - - + +
204B LYS* 3.7 42.6 - - + +
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Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B VAL* 3.9 9.8 - - + -
133B LEU* 1.3 68.6 - - - +
135B GLY* 1.3 59.5 - - - +
136B ASP* 3.0 10.5 + - - +
137B LYS* 2.8 25.1 + - + +
139B ALA* 4.6 13.2 - - + +
141B VAL* 4.4 20.6 - - - +
153B GLU* 5.4 4.2 + - - -
158B ALA* 5.8 1.4 - - - +
159B SER* 3.3 43.1 + - - +
160B GLY* 4.1 5.2 - - - -
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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