Contacts of the helix formed by residues 132 - 140 (chain B) in PDB entry 2XI4
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 GLY 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B TRP* 3.4 21.9 - - - -
130B TYR 3.0 6.5 + - - -
131B ASN* 1.3 74.4 + - - +
133B LYS* 1.3 63.3 + - - +
134B TYR 3.3 1.5 + - - -
135B LEU* 3.4 3.7 + - - -
136B ALA* 3.1 24.6 + - - +
143B LEU* 3.3 30.7 - - - +
448B PHE* 4.4 3.4 - - - -
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 4.4 8.7 - - + +
21B PRO* 2.8 35.0 + - - +
22B VAL* 3.7 14.3 - - + +
27B ILE* 3.8 8.0 - - + +
100B TRP* 3.7 22.9 - - + -
131B ASN* 3.3 20.4 + - - +
132B GLY* 1.3 79.0 - - - +
134B TYR* 1.3 103.3 + - + +
137B TYR* 3.1 26.9 + - - +
1002B CL 3.7 14.5 - - - +
1003B PEG 4.0 15.5 + - - +
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Residues in contact with TYR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL* 3.9 9.9 - - + -
23B LEU* 3.6 36.8 - - + -
131B ASN* 4.1 22.1 + - + -
132B GLY 3.3 1.0 - - - -
133B LYS* 1.3 112.5 + - + +
135B LEU* 1.3 54.4 + - - +
137B TYR* 4.0 0.3 - - - +
138B THR* 2.7 39.7 + - - +
448B PHE 3.2 24.9 - - - +
449B GLY* 4.0 15.7 - - - +
450B LEU* 4.5 13.0 - - + -
452B LEU* 5.4 1.3 - - + -
453B VAL* 3.5 27.0 - - + +
470B MET* 4.4 2.5 - - - -
1002B CL 3.6 10.4 - - + +
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Residues in contact with LEU 135 (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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112B MET* 4.4 10.5 - - + -
132B GLY 3.4 7.6 + - - +
134B TYR* 1.3 74.5 - - - +
136B ALA* 1.3 67.1 + - - +
139B GLU* 2.9 43.5 + - + +
141B VAL* 3.8 7.5 - - + +
143B LEU* 3.5 28.7 - - + -
197B PHE* 4.1 18.2 - - + -
447B VAL* 3.9 15.7 - - + +
448B PHE* 4.2 13.2 + - + -
470B MET* 3.8 44.2 - - + +
473B TRP* 5.5 2.2 - - + -
474B ALA* 4.8 3.6 - - + -
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Residues in contact with ALA 136 (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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27B ILE* 3.9 9.9 - - + -
100B TRP* 3.8 26.7 - - + +
102B PRO* 3.6 5.4 - - + +
132B GLY 3.1 17.3 + - - +
135B LEU* 1.3 78.1 - - - +
137B TYR* 1.3 55.7 + - - +
140B GLU* 2.9 25.5 + - - -
141B VAL* 3.1 34.0 + - - +
143B LEU* 4.0 6.6 - - + +
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Residues in contact with TYR 137 (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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22B VAL* 4.0 25.4 - - + -
23B LEU* 4.1 31.5 + - + -
25B SER* 3.5 32.3 - - - -
26B HIS 4.9 0.4 - - - -
27B ILE* 3.9 21.4 - - + +
102B PRO* 5.3 2.0 - - - +
133B LYS 3.1 20.9 + - - +
134B TYR 4.0 0.4 - - - +
136B ALA* 1.3 80.8 - - - +
138B THR* 1.3 77.1 + - - +
140B GLU* 3.5 13.7 + - - +
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Residues in contact with THR 138 (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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23B LEU* 4.3 1.9 - - - +
134B TYR 2.7 21.3 + - - -
135B LEU 4.2 1.1 - - - -
137B TYR* 1.3 92.1 - - - +
139B GLU* 1.3 76.8 + - - +
140B GLU* 3.8 4.3 + - - +
452B LEU* 3.7 17.2 - - - +
467B ARG* 4.0 24.5 - - + +
470B MET* 4.1 18.6 - - + +
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Residues in contact with GLU 139 (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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135B LEU* 2.9 26.9 + - + +
138B THR* 1.3 93.9 - - + +
140B GLU* 1.3 72.8 + - - +
141B VAL* 3.3 4.7 + - + +
467B ARG 4.4 2.8 - - - +
470B MET* 3.6 13.4 - - + +
471B HIS* 2.7 52.5 + - - +
474B ALA* 3.5 29.3 - - + +
475B THR* 4.6 0.3 + - - -
478B LYS* 3.5 21.1 + - - +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PRO* 3.9 15.5 - - + -
106B PRO* 5.8 0.5 - - - +
109B THR* 3.5 21.1 + - - +
136B ALA 2.9 12.2 + - - -
137B TYR 3.9 10.3 - - - +
138B THR 3.4 5.1 - - - +
139B GLU* 1.3 81.9 - - - +
141B VAL* 1.3 60.9 + - - +
478B LYS* 4.3 11.0 + - - +
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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