Contacts of the strand formed by residues 128 - 133 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171C GLU* 3.8 19.4 + - - -
43D PHE 3.4 8.5 - - - +
44D TYR* 4.6 0.4 - - - -
45D PRO* 3.9 31.6 - - + +
50D PHE 4.1 10.1 + - - -
51D VAL* 4.2 6.5 - - - +
52D CYS* 4.7 1.6 - - - +
55D GLU* 3.8 31.0 + - - +
127D PHE* 1.3 71.3 - - - +
129D GLY* 1.3 59.3 + - - +
144D VAL* 3.3 7.0 - - - +
145D ASN* 2.9 46.1 + - - +
146D ASP* 5.0 5.7 - - - +
147D LEU 3.3 21.5 + - - +
148D PRO* 3.7 30.2 - - - +
149D VAL 4.3 5.3 - - - +
151D ARG* 3.5 14.7 + - - +
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Residues in contact with GLY 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PHE* 3.2 7.3 - - - +
43D PHE* 2.9 35.7 + - - +
118D VAL* 4.4 7.9 - - - -
127D PHE 3.5 3.0 + - - -
128D ARG* 1.3 75.7 - - - +
130D LEU* 1.3 59.3 + - - -
131D PHE* 4.0 17.0 - - - -
143D THR 3.2 7.6 - - - -
144D VAL* 4.5 0.2 - - - -
151D ARG* 3.6 5.3 + - - -
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Residues in contact with LEU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D VAL* 4.0 27.4 - - + -
41D PHE 3.9 0.9 - - - +
42D PHE* 4.3 9.9 - - + -
59D PHE* 5.5 2.5 - - + -
129D GLY* 1.3 74.3 - - - -
131D PHE* 1.3 68.3 + - - +
132D ILE* 4.4 15.9 - - + -
141D GLN* 3.7 21.4 - - - +
142D ILE* 3.4 4.9 - - - -
143D THR* 2.8 35.6 + - - +
151D ARG* 3.6 38.1 - - - +
156D THR* 4.6 15.3 - - + +
159D LEU* 4.4 7.2 - - + -
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Residues in contact with PHE 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ALA* 4.6 2.0 - - + -
39D VAL 3.5 2.6 - - - +
40D VAL* 3.6 3.3 - - - -
41D PHE* 2.8 61.4 + + + +
43D PHE* 4.3 9.9 - + - -
116D TYR* 3.3 55.9 - + + -
118D VAL* 3.6 18.4 - - + -
129D GLY* 4.0 20.9 - - - -
130D LEU* 1.3 74.8 - - - +
132D ILE* 1.3 65.4 + - - +
133D ILE* 4.5 3.8 - - + -
139D LEU* 3.9 16.6 - - + -
141D GLN 3.3 3.8 - - - -
142D ILE* 3.8 39.9 - - + -
144D VAL* 4.9 0.2 - - + -
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Residues in contact with ILE 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D TYR* 3.9 29.2 - - + -
39D VAL 3.6 3.1 - - - +
40D VAL* 4.1 22.4 - - + -
130D LEU* 4.4 14.8 - - + -
131D PHE* 1.3 79.2 - - - +
133D ILE* 1.3 57.0 + - - +
139D LEU* 3.5 4.2 - - - +
140D ARG* 2.7 34.7 + - + -
141D GLN* 3.0 26.3 + - + +
156D THR* 4.7 3.4 - - + -
159D LEU* 3.8 30.1 - - + -
160D VAL* 4.4 11.7 - - + -
163D PHE* 3.9 16.4 - - + -
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Residues in contact with ILE 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ALA* 3.7 24.7 - - + -
31D LEU* 4.0 26.7 - - + -
38D TYR* 3.3 8.2 - - - -
39D VAL* 2.8 48.6 + - + +
41D PHE* 4.0 24.5 - - + -
116D TYR* 4.8 0.9 - - + +
131D PHE* 4.5 8.1 - - + -
132D ILE* 1.3 77.6 - - - +
134D ASP* 1.3 64.5 + - - +
137D GLY* 3.5 35.2 - - - +
138D ILE 3.4 4.5 - - - +
139D LEU* 3.8 9.4 - - + -
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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