Contacts of the strand formed by residues 128 - 133 (chain B) in PDB entry 4XCS
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
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Residue Dist Surf HB Arom Phob DC
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43B PHE 3.4 6.5 - - - +
44B TYR* 4.9 1.1 - - + +
45B PRO* 3.9 27.7 - - + +
50B PHE 3.9 15.4 + - - -
51B VAL* 3.9 19.0 - - - +
52B CYS* 4.5 4.0 - - - +
55B GLU* 4.5 6.5 + - - +
127B PHE* 1.3 72.7 - - - +
129B GLY* 1.3 58.3 + - - +
143B THR 3.7 0.7 - - - +
144B VAL* 3.3 4.7 - - - +
145B ASN* 3.0 46.9 + - - +
146B ASP* 5.0 5.2 - - - +
147B LEU 3.2 21.7 + - - +
148B PRO* 3.7 33.1 - - - +
149B VAL 4.2 8.8 + - - -
151B ARG* 3.9 25.1 - - - +
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Residues in contact with GLY 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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42B PHE* 3.2 2.8 - - - -
43B PHE* 2.9 33.9 + - - +
118B VAL* 4.4 8.1 - - - -
127B PHE 3.5 2.8 + - - -
128B ARG* 1.3 75.3 - - - +
130B LEU* 1.3 59.5 + - - -
131B PHE* 3.9 17.9 - - - -
143B THR 3.2 7.6 - - - -
151B ARG* 3.2 10.8 + - - +
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Residues in contact with LEU 130 (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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40B VAL* 3.9 27.8 - - + -
41B PHE 3.8 0.7 - - - -
42B PHE* 4.4 8.3 - - + -
59B PHE* 5.7 1.6 - - + -
129B GLY* 1.3 74.1 - - - -
131B PHE* 1.3 66.7 + - - +
132B ILE* 4.5 17.3 - - + -
141B GLN* 3.5 20.8 - - - +
142B ILE* 3.3 5.9 - - - -
143B THR* 2.8 48.6 + - + +
151B ARG* 3.7 33.6 - - + +
156B THR* 4.5 14.1 - - + +
159B LEU* 4.6 6.1 - - + -
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Residues in contact with PHE 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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6B ALA* 4.7 2.9 - - + -
39B VAL 3.4 3.1 - - - +
40B VAL* 3.5 3.1 - - - -
41B PHE* 2.8 62.3 + + + +
43B PHE* 4.3 11.0 - + - -
116B TYR* 3.4 54.5 - + + -
118B VAL* 3.6 18.2 - - + -
129B GLY* 3.9 21.3 - - - -
130B LEU* 1.3 75.6 - - - +
132B ILE* 1.3 64.7 + - - +
133B ILE* 4.0 5.6 - - + -
139B LEU* 3.9 15.9 - - + -
141B GLN 3.3 3.4 - - - -
142B ILE* 3.8 38.4 - - + -
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 3.9 29.2 - - + -
39B VAL 3.6 2.9 - - - +
40B VAL* 4.1 21.3 - - + -
130B LEU* 4.5 15.7 - - + -
131B PHE* 1.3 78.8 - - - +
133B ILE* 1.3 56.5 + - - +
139B LEU* 3.4 4.2 - - - +
140B ARG* 2.7 34.1 + - + -
141B GLN* 3.1 26.0 + - + +
156B THR* 4.7 3.4 - - + -
159B LEU* 3.8 29.6 - - + -
160B VAL* 4.3 11.9 - - + -
163B PHE* 4.0 16.6 - - + -
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Residues in contact with ILE 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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12B ALA* 3.7 26.2 - - + -
31B LEU* 4.2 20.4 - - + -
38B TYR* 3.3 8.8 - - - -
39B VAL* 2.9 47.1 + - + +
41B PHE* 3.9 30.7 - - + -
116B TYR* 4.9 1.1 - - + +
131B PHE* 4.4 9.4 - - + -
132B ILE* 1.3 77.4 - - - +
134B ASP* 1.4 66.4 + - - +
137B GLY* 3.6 31.6 - - - +
138B ILE 3.4 4.3 - - - +
139B LEU* 3.8 9.9 - - + -
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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