Contacts of the strand formed by residues 128 - 133 (chain C) in PDB entry 2VRF
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 ILE 128 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C LEU* 3.8 18.6 - - + +
127C GLY* 1.3 79.1 - - - +
129C SER* 1.3 63.7 + - - +
130C ILE* 4.0 15.9 - - + -
142C ILE* 4.1 19.7 - - + -
144C LYS 3.1 14.6 - - - +
145C ILE* 4.4 9.0 - - + -
146C PHE* 3.9 7.1 - - - -
151C ALA* 3.3 32.5 - - + -
157C LEU* 4.8 7.0 - - + -
163C ILE* 4.2 8.7 - - + -
192C LEU* 5.5 2.9 - - + -
203D VAL* 3.5 3.6 - - - -
204D VAL* 2.9 50.4 + - + +
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Residues in contact with SER 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C ILE* 1.3 72.0 - - - +
130C ILE* 1.3 64.0 + - - +
142C ILE* 3.5 6.6 - - - +
143C SER* 2.8 39.3 + - - -
144C LYS* 3.0 21.0 + - - +
146C PHE* 3.5 19.4 - - - -
201D ASN* 4.6 9.3 - - - +
202D THR 3.2 12.1 - - - -
203D VAL* 3.5 14.0 - - - +
204D VAL 4.7 0.2 - - - +
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Residues in contact with ILE 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C ILE* 4.0 12.3 - - + -
129C SER* 1.3 80.0 - - - +
131C LYS* 1.3 60.3 + - - +
140C ILE* 3.9 17.7 - - + -
141C LEU 3.3 9.6 - - - +
142C ILE* 4.6 0.4 - - - -
143C SER* 3.7 2.2 - - - -
163C ILE* 3.8 28.5 - - + -
176C HIS* 3.4 12.5 - - + +
179C ALA* 4.1 4.5 - - + -
180C VAL* 3.8 31.2 - - + +
183C LEU* 3.8 22.0 - - + -
201D ASN* 3.3 6.1 - - - -
202D THR 2.9 35.6 + - - +
204D VAL* 4.3 7.6 - - + -
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Residues in contact with LYS 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C ILE* 1.3 73.2 - - - +
132C GLY* 1.3 63.8 + - - +
138C MET* 4.9 7.9 - - + -
139C PRO 3.6 0.2 - - - +
140C ILE* 3.5 6.7 - - - +
141C LEU* 2.9 61.5 + - + +
142C ILE 5.3 1.3 - - - -
143C SER* 3.8 21.4 - - - +
176C HIS* 3.8 4.7 - - - -
131D LYS* 5.4 7.3 - - - +
199D GLU* 6.2 4.0 - - + -
200D VAL 3.2 22.7 - - - +
201D ASN* 3.5 10.5 - - - +
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Residues in contact with GLY 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C LYS* 1.3 79.0 - - - +
133C GLY* 1.3 59.8 + - - -
135C GLU* 4.4 1.2 - - - +
136C ASN* 5.1 10.1 + - - +
138C MET* 4.0 21.0 - - - +
139C PRO 3.3 11.2 - - - -
140C ILE* 4.2 3.0 - - - +
176C HIS* 3.2 28.2 + - - +
200D VAL* 4.4 1.6 + - - +
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Residues in contact with GLY 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C GLY* 1.3 74.7 - - - -
134C ARG* 1.3 60.8 + - - -
135C GLU* 3.1 12.3 - - - -
136C ASN* 3.0 20.6 + - - +
138C MET 3.1 27.5 + - - +
139C PRO 3.5 3.4 + - - -
140C ILE* 3.8 10.7 - - - +
174C ALA 3.4 10.3 - - - -
176C HIS 3.9 2.2 - - - -
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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