Contacts of the strand formed by residues 126 - 130 (chain H) in PDB entry 2VDK
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 SER 126 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124H ALA 3.8 2.5 + - - -
125H PRO* 1.3 73.2 - - - +
127H VAL* 1.3 60.1 + - - +
128H TYR* 3.5 32.9 + - - -
147H LEU 3.4 4.7 - - - +
148H VAL* 3.5 1.6 - - - -
149H LYS* 2.9 39.7 + - - +
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Residues in contact with VAL 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H PRO* 3.9 11.8 + - + +
126H SER* 1.3 75.7 - - - +
128H TYR* 1.3 71.2 + - - +
146H CYS* 3.5 27.6 - - - -
147H LEU 3.5 4.3 - - - +
148H VAL* 4.8 1.8 - - + -
201H CYS* 4.4 0.9 - - - -
203H VAL* 3.8 37.9 - - + -
212H VAL* 4.0 23.6 - - + +
214H LYS* 3.5 43.8 + - + +
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Residues in contact with TYR 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H SER* 3.5 31.7 + - - -
127H VAL* 1.3 83.9 - - - +
129H PRO* 1.3 66.9 - - - +
130H LEU* 3.7 4.6 + - + +
146H CYS* 3.5 7.2 - - - -
147H LEU* 2.9 63.4 + - + +
149H LYS* 4.5 10.8 - - + -
121L SER* 3.4 26.5 - - - +
123L GLU* 3.9 13.2 - - + -
124L GLN* 3.5 43.8 - - + +
127L SER* 3.6 20.1 + - - -
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Residues in contact with PRO 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H TYR* 1.3 85.5 - - + +
130H LEU* 1.3 61.0 + - - +
131H ALA* 3.9 2.7 + - + -
145H GLY 4.0 0.9 - - - +
146H CYS* 4.9 1.1 - - - -
214H LYS* 4.2 20.2 - - + -
215H LYS 4.0 15.9 - - - +
216H ILE* 3.4 27.6 - - + -
217H GLU 5.2 1.8 - - - +
219H ARG* 4.7 1.7 + - - -
121L SER* 3.5 19.1 - - - -
123L GLU* 3.4 37.7 - - - +
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Residues in contact with LEU 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H TYR* 3.8 14.4 - - + +
129H PRO* 1.3 79.8 - - - +
131H ALA* 1.3 61.4 + - - +
144H LEU* 3.7 5.2 - - - +
145H GLY* 2.9 40.1 + - - +
146H CYS 3.6 24.9 - - - +
147H LEU* 3.9 11.9 - - + +
216H ILE* 3.7 3.5 - - - +
219H ARG* 4.5 2.9 - - - +
118L PHE* 3.4 23.3 - - + -
119L PRO 4.5 15.3 - - - +
120L PRO* 5.9 0.2 - - + -
121L SER* 5.0 4.5 - - - +
131L SER 5.7 1.6 - - - +
133L VAL* 4.0 38.4 - - + -
135L PHE* 4.4 6.3 - - + -
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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