Contacts of the strand formed by residues 128 - 132 (chain B) in PDB entry 3CFV
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 ARG 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU 5.3 2.6 + - - -
45B THR* 3.8 8.4 + - - +
126B VAL* 3.3 3.5 - - - +
127B ASN* 1.3 79.6 + - - +
129B ALA* 1.3 63.1 + - - +
130B ARG* 3.3 36.8 - - - +
140B ALA 3.8 0.2 - - - +
141B THR* 3.1 7.3 - - - -
142B LYS* 2.9 30.1 + - + +
180B TYR* 3.3 53.3 + - - +
181B GLY* 4.1 0.6 - - - -
182B LEU* 4.0 18.9 + - + +
230B GLU 5.1 1.2 + - - -
231B ASP* 3.6 25.5 + - - -
320B PHE 5.3 5.3 + - - -
321B GLN* 4.0 22.3 + - - +
377B SER 4.9 8.9 + - - -
378B ASP* 4.5 5.1 + - - -
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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
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45B THR* 3.2 16.9 + - + +
46B VAL 5.3 0.2 - - - -
47B GLN* 3.6 8.0 - - - +
66B VAL* 3.9 15.4 - - + +
78B LEU* 3.6 31.0 - - + -
126B VAL* 3.9 9.4 - - + -
128B ARG* 1.3 76.2 - - - +
130B ARG* 1.3 81.0 + - - +
139B ILE* 4.2 1.8 - - + -
140B ALA 3.3 7.9 - - - +
141B THR* 4.0 1.1 - - + -
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Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR* 2.9 27.9 + - - -
46B VAL 3.3 14.8 + - - -
47B GLN* 3.0 28.6 + - - +
66B VAL* 5.8 0.2 - - - -
128B ARG* 3.3 29.1 - - - +
129B ALA* 1.3 86.4 + - - +
131B TYR* 1.3 61.4 + - - +
139B ILE* 3.4 5.7 - - - +
140B ALA 2.9 30.9 + - - -
182B LEU* 3.9 35.6 + - + +
183B SER* 5.4 0.7 - - - +
184B TRP* 3.0 23.9 + - + +
321B GLN* 4.6 6.3 + - - -
323B HIS* 4.8 11.5 + - - -
378B ASP* 3.1 17.6 + - - -
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Residues in contact with TYR 131 (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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47B GLN* 2.9 48.6 + - + +
48B TRP 3.1 25.5 + - - -
49B LEU* 3.9 16.8 - - + -
50B PRO* 3.7 33.7 - - + +
66B VAL* 5.0 2.2 - - + +
130B ARG* 1.3 74.5 - - - +
132B MSE 1.3 72.3 + - - +
133B PRO* 3.4 26.3 - - + +
136B PRO* 3.7 27.8 - - + +
138B ILE 3.5 5.6 - - - +
139B ILE* 4.2 6.7 - - + -
184B TRP* 3.2 11.9 - - - +
383B PRO* 5.7 2.9 - - - +
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Residues in contact with MSE 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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131B TYR* 1.3 71.7 - - - +
133B PRO* 1.3 70.4 - - + +
134B GLN* 3.4 16.6 - - + +
135B ASN* 2.9 65.6 + - + +
136B PRO* 3.2 4.9 - - - +
138B ILE* 2.9 28.1 + - + +
184B TRP* 3.5 45.2 - - + +
189B SER* 3.8 17.9 - - - +
190B GLY* 4.0 16.8 - - - +
206B ILE* 4.2 9.4 - - - -
207B ASN* 6.0 1.3 - - - +
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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