Contacts of the helix formed by residues 90 - 101 (chain B) in PDB entry 1XJP
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 ASN 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B GLU* 3.1 16.0 + - - +
26B LYS* 3.7 25.3 - - - +
89B GLN* 1.3 81.5 - - - +
91B LEU* 1.3 54.3 + - - +
92B THR* 3.0 26.6 + - - -
93B VAL* 2.6 55.2 + - + +
94B LYS* 3.0 2.5 + - - -
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Residues in contact with LEU 91 (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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89B GLN* 2.7 23.5 + - + +
90B ASN* 1.3 70.7 + - - +
92B THR* 1.3 61.1 + - - +
94B LYS* 3.2 19.5 + - + +
95B LEU* 3.0 31.3 + - + +
210B ASN 4.8 1.3 - - - +
211B GLY* 3.0 30.1 - - - +
212B VAL* 3.6 19.5 - - + -
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Residues in contact with THR 92 (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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90B ASN* 2.8 17.3 + - - -
91B LEU* 1.3 77.7 - - - +
93B VAL* 1.3 61.1 + - + +
95B LEU* 3.7 11.8 + - + +
96B GLN* 3.1 27.9 + - - +
389B PRO* 5.2 4.0 - - + -
392B LEU* 4.0 22.1 - - + +
563B SER* 5.1 8.8 + - - -
564B GLU* 5.4 2.1 + - - -
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Residues in contact with VAL 93 (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 GLU* 3.8 6.7 - - - +
25B ALA* 5.6 4.5 - - + -
26B LYS* 4.2 24.2 - - + -
29B LEU* 3.9 15.6 - - + +
88B ILE* 3.4 24.9 - - + -
90B ASN* 2.6 51.5 + - + +
92B THR* 1.3 73.3 - - + +
94B LYS* 1.3 59.2 + - - +
95B LEU 3.3 0.2 - - - -
96B GLN* 3.6 11.8 + - - +
97B LEU* 3.0 31.7 + - + +
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Residues in contact with LYS 94 (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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85B LEU* 4.5 21.5 - - + +
88B ILE* 4.2 19.7 - - + +
89B GLN 5.7 0.9 - - - +
90B ASN 3.0 5.9 + - - +
91B LEU* 3.2 25.3 + - + +
93B VAL* 1.3 78.1 - - - +
95B LEU* 1.3 61.0 + - - +
97B LEU* 3.5 5.9 - - + +
98B GLN* 2.5 66.6 + - + +
210B ASN* 4.3 28.5 + - - +
211B GLY* 4.9 3.6 - - - +
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Residues in contact with LEU 95 (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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91B LEU* 3.0 20.7 + - + +
92B THR* 3.7 13.5 - - - +
94B LYS* 1.3 79.6 - - - +
96B GLN* 1.3 57.1 + - - +
98B GLN* 3.0 20.2 + - - +
99B ALA* 2.9 29.9 + - - +
392B LEU* 4.2 15.0 - - + -
562B LYS* 3.7 18.8 - - + +
563B SER* 3.6 27.6 - - - +
564B GLU* 5.4 1.6 - - - -
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Residues in contact with GLN 96 (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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29B LEU* 3.9 25.5 - - + +
33B ASN* 3.5 19.4 + - - +
92B THR* 3.1 25.1 + - - +
93B VAL* 3.9 10.6 - - - +
94B LYS 3.3 0.4 - - - -
95B LEU* 1.3 78.5 - - - +
97B LEU* 1.3 64.3 + - - +
99B ALA* 3.3 2.8 + - - +
100B LEU* 3.1 20.0 + - - +
389B PRO* 3.4 35.6 - - + +
391B LEU* 3.5 32.6 - - + +
392B LEU* 3.9 19.7 - - + +
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Residues in contact with LEU 97 (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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25B ALA* 4.8 7.4 - - + -
28B PHE* 4.6 11.0 - - + -
29B LEU* 4.6 9.6 - - + +
80B ALA* 3.9 26.2 - - + +
83B TYR* 3.8 22.2 - - + +
85B LEU* 4.9 2.7 - - - -
88B ILE* 3.7 36.1 - - + -
93B VAL* 3.0 20.1 + - + +
94B LYS* 3.6 5.2 - - + +
96B GLN* 1.3 77.0 - - - +
98B GLN* 1.3 64.2 + - - +
100B LEU* 3.3 4.3 + - - +
101B GLN* 3.0 57.8 + - - +
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Residues in contact with GLN 98 (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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94B LYS* 2.5 51.7 + - + +
95B LEU* 3.1 22.0 - - - +
97B LEU* 1.3 76.1 - - - +
99B ALA* 1.3 65.9 + - - +
101B GLN* 3.5 13.9 + - - +
102B GLN* 4.0 9.9 + - - +
208B GLU 5.8 0.3 - - - +
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Residues in contact with ALA 99 (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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95B LEU 2.9 14.9 + - - +
96B GLN* 3.6 8.5 - - - +
98B GLN* 1.3 74.8 - - - +
100B LEU* 1.3 62.5 + - - +
102B GLN* 3.5 24.2 - - - +
391B LEU* 4.2 24.9 - - + +
392B LEU* 6.4 0.4 - - + -
562B LYS* 6.1 1.6 - - - +
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Residues in contact with LEU 100 (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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28B PHE* 3.7 31.4 - - + -
29B LEU* 4.1 7.2 - - + -
32B PHE* 3.6 43.5 - - + -
73B LEU* 4.8 11.7 - - + +
76B GLN* 4.6 9.9 - - + +
77B SER* 2.4 39.3 + - - +
80B ALA* 4.3 8.5 - - + -
96B GLN 3.1 9.9 + - - +
97B LEU 3.7 4.5 - - - +
99B ALA* 1.3 75.3 - - - +
101B GLN* 1.3 51.7 + - - +
102B GLN 2.9 10.0 + - - +
391B LEU* 3.7 25.4 - - + -
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Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B SER* 3.8 2.5 - - - +
80B ALA* 3.7 7.8 + - + -
81B GLN* 3.3 58.3 + - - +
83B TYR 3.6 15.8 + - - +
85B LEU* 4.7 23.2 - - - +
97B LEU* 3.0 50.6 + - - +
98B GLN* 3.5 8.6 + - - +
100B LEU* 1.3 70.5 - - - +
102B GLN* 1.3 57.3 + - - +
103B ASN* 3.7 3.5 + - - -
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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