Contacts of the helix formed by residues 91 - 101 (chain B) in PDB entry 3UXP
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 ASP 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B PHE* 5.6 1.2 - - - -
29B VAL* 5.9 0.2 - - - +
87B LYS 3.0 9.9 + - - +
88B ILE* 3.2 8.3 + - - +
90B GLN* 1.3 77.6 - - - +
92B ASP* 1.3 68.7 + - - +
93B THR* 3.4 13.8 + - - +
94B SER* 3.0 34.3 + - - +
95B SER* 2.9 28.0 + - - -
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Residues in contact with ASP 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 GLN 3.5 5.1 + - - -
91B ASP* 1.3 74.8 + - - +
93B THR* 1.3 56.9 + - - +
95B SER* 3.5 5.0 + - - -
96B SER* 2.8 39.8 + - - -
120B LYS* 2.5 37.9 + - - +
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Residues in contact with THR 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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29B VAL* 6.0 2.0 - - + -
91B ASP* 3.4 12.5 + - - +
92B ASP* 1.3 82.3 + - - +
94B SER* 1.3 63.3 + - - +
96B SER* 3.2 2.6 + - - -
97B ILE* 3.1 41.1 + - + +
115B VAL* 4.0 21.4 - - + +
120B LYS* 4.5 1.7 + - - +
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Residues in contact with SER 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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25B PHE* 4.2 17.3 - - - -
29B VAL* 3.5 31.2 - - - +
88B ILE* 3.1 15.5 + - - +
91B ASP* 3.0 34.0 + - - +
92B ASP 3.3 0.2 - - - -
93B THR* 1.3 79.7 - - - +
95B SER* 1.3 59.3 + - - +
97B ILE 3.5 0.9 + - - -
98B ASN* 3.1 34.2 + - - -
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Residues in contact with SER 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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88B ILE 4.6 6.5 - - - -
89B ARG* 5.0 8.3 - - - -
91B ASP 2.9 19.8 + - - -
92B ASP* 3.9 4.7 + - - -
94B SER* 1.3 76.7 + - - +
96B SER* 1.3 62.4 + - - +
98B ASN* 4.0 11.6 + - - +
99B PHE* 3.6 17.2 + - - +
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Residues in contact with SER 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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92B ASP* 2.8 23.1 + - - -
93B THR 3.8 3.6 - - - -
95B SER* 1.3 77.9 + - - +
97B ILE* 1.3 66.5 + - - +
98B ASN 3.2 0.9 - - - -
99B PHE* 3.1 14.5 + - - +
100B LEU* 3.2 18.7 + - - +
115B VAL* 4.2 9.9 - - - -
120B LYS* 3.3 47.0 + - - +
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Residues in contact with ILE 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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28B ASN* 3.4 30.7 - - + +
29B VAL* 4.0 21.1 - - + -
93B THR* 3.1 33.2 + - + +
94B SER 3.8 4.0 - - - +
96B SER* 1.3 75.9 - - - +
98B ASN* 1.3 63.5 + - - +
100B LEU* 5.0 0.2 - - - -
101B THR* 3.2 25.0 + - - +
108B PRO* 4.4 5.2 - - + +
111B ALA* 4.1 22.8 - - + +
112B ARG* 4.2 20.2 - - + +
115B VAL* 3.5 22.0 - - + -
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Residues in contact with ASN 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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24B ASN* 4.6 8.8 - - - +
25B PHE* 5.1 9.5 - - - +
28B ASN* 2.9 35.1 + - - +
29B VAL* 4.8 5.6 - - - +
88B ILE* 5.2 8.3 - - - +
94B SER* 3.1 27.6 + - - +
95B SER* 4.1 9.4 - - - +
96B SER 3.2 0.2 - - - -
97B ILE* 1.3 77.2 - - - +
99B PHE* 1.3 61.4 + - - +
101B THR* 3.3 22.1 - - - +
102B ARG* 3.8 7.2 + - - +
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Residues in contact with PHE 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 SER 3.6 12.0 + - - +
96B SER* 3.1 10.5 + - - +
98B ASN* 1.3 74.1 - - - +
100B LEU* 1.3 63.5 + - + +
101B THR 3.1 1.6 - - - -
102B ARG* 2.6 75.1 + - - +
103B VAL* 4.8 0.5 - - - +
120B LYS 3.4 24.5 - - - +
121B THR* 4.4 2.0 - - - -
122B LEU* 3.6 42.2 - - + -
143B PHE* 4.0 14.6 - + - -
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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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96B SER 3.2 8.4 + - - +
99B PHE* 1.3 85.3 - - + +
101B THR* 1.3 63.1 + - - +
103B VAL* 2.9 23.3 + - - +
106B ILE* 3.3 21.2 - - + +
111B ALA* 4.1 22.0 - - + +
114B LEU* 3.7 28.9 - - + -
115B VAL* 4.3 6.7 - - + -
119B ILE* 3.6 21.5 - - + +
120B LYS* 3.3 31.9 - - - +
121B THR 4.7 0.4 - - - +
125B LEU* 4.3 26.0 - - + -
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Residues in contact with THR 101 (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 LYS* 6.3 0.9 - - - -
28B ASN* 4.2 29.1 + - - +
97B ILE* 3.2 13.2 + - - +
98B ASN* 3.3 18.8 - - - +
100B LEU* 1.3 76.2 - - - +
102B ARG* 1.3 58.7 + - + +
103B VAL 3.0 0.6 + - - -
106B ILE* 4.0 10.2 - - - +
107B GLY* 3.3 20.4 + - - -
108B PRO* 4.4 2.8 - - - +
111B ALA* 4.4 0.2 - - - +
338B NA 2.1 34.3 - - - -
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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