Contacts of the strand formed by residues 129 - 135 (chain A) in PDB entry 4KXA
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 THR 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A PHE* 4.2 17.1 - - + -
125A LEU* 3.7 24.7 - - + -
127A ALA 3.7 11.7 - - - +
128A PRO* 1.3 75.2 - - - +
130A ARG* 1.3 58.3 + - - +
131A TYR* 2.7 33.9 + - - +
132A LEU* 3.8 8.7 - - + -
133A TRP* 4.1 8.3 - - - -
173A ALA* 5.8 0.5 - - - +
176A GLU* 3.2 20.6 + - - +
177A LEU 3.3 12.7 + - - -
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Residues in contact with ARG 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A THR* 1.3 73.4 + - - +
131A TYR* 1.3 92.0 + - + +
158A ARG* 3.3 35.4 - - - +
172A GLU* 2.5 36.6 + - - +
173A ALA* 3.2 48.7 + - - +
175A GLU 4.3 9.8 - - - +
176A GLU* 3.6 29.1 + - + +
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Residues in contact with TYR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A SER 5.6 1.5 + - - -
86A GLY* 6.1 0.4 - - - -
88A TRP* 3.5 40.5 - + + -
129A THR* 2.7 23.1 + - - +
130A ARG* 1.3 119.0 + - + +
132A LEU* 1.3 69.1 + - - +
133A TRP* 3.2 18.7 - - + -
161A PHE* 4.2 4.0 - + - -
170A VAL* 3.9 20.4 - - + -
171A VAL 3.4 3.6 - - - -
172A GLU* 3.4 39.1 + - + -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A VAL* 4.4 24.5 - - + -
123A ILE* 4.5 20.6 - - + -
125A LEU* 4.2 16.4 - - + -
129A THR* 3.8 19.3 - - + -
131A TYR* 1.3 83.7 - - - +
133A TRP* 1.3 61.7 + - - +
134A LEU* 5.6 1.6 - - - +
147A LEU* 3.8 36.1 - - + -
169A VAL 4.0 0.7 - - - +
170A VAL* 3.6 0.6 - - - -
171A VAL* 2.9 48.4 + - + +
186A TYR* 5.5 3.1 - - + -
188A LEU* 5.2 9.6 - - + -
234A PHE* 6.0 1.1 - - + -
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Residues in contact with TRP 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLN* 3.4 39.1 + - + -
88A TRP* 3.7 22.6 - + + +
93A LEU* 4.1 4.9 - - + +
94A PRO* 3.4 46.5 - - + +
96A PHE* 4.4 10.1 - + - -
97A VAL* 5.4 6.1 - - + +
129A THR* 4.1 5.8 - - - -
131A TYR* 3.2 37.5 - - + -
132A LEU* 1.3 75.7 - - - +
134A LEU* 1.3 67.1 + - - +
168A TYR* 3.6 40.3 + + + -
169A VAL 3.4 5.4 - - - +
170A VAL* 3.4 26.7 - - + -
234A PHE* 3.6 17.0 - - - -
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 4.3 5.8 - - - -
121A ILE* 3.5 31.9 - - + -
132A LEU 5.6 0.9 - - - +
133A TRP* 1.3 80.1 - - - +
135A HIS* 1.3 63.0 + - - +
168A TYR* 3.4 12.4 - - - -
169A VAL* 2.9 52.1 + - + +
171A VAL* 6.4 0.7 - - + -
188A LEU* 4.6 8.5 - - + -
190A MET* 4.0 18.4 - - + -
232A PRO* 4.1 3.4 - - + -
233A CYS* 3.5 32.3 - - - +
234A PHE* 3.9 21.5 - - + -
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Residues in contact with HIS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PHE* 4.6 6.1 + - - -
93A LEU* 3.5 35.1 - - + +
134A LEU* 1.3 69.9 - - - +
136A LEU* 1.3 64.4 + - - +
166A GLN 4.0 5.4 + - - -
167A GLU 3.3 14.6 - - - -
168A TYR* 3.5 19.1 + + - -
228A ARG* 3.3 59.3 + - + +
232A PRO* 3.4 5.2 - - - +
233A CYS 2.8 37.8 + - - +
235A ASP* 3.1 24.7 + - + +
236A GLU* 4.3 7.6 - - + -
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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