Contacts of the helix formed by residues 92 - 101 (chain A) in PDB entry 3UXA
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 SER 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ARG* 4.5 3.8 - - - +
54A ARG* 4.6 1.9 + - - -
83A LEU 4.1 0.4 + - - +
84A THR* 3.9 17.7 - - - +
86A GLU* 5.0 3.8 - - - -
90A ASN 5.5 0.2 - - - -
91A GLY* 1.3 75.3 - - - -
93A TYR* 1.3 64.8 + - - +
94A GLU* 3.1 15.0 + - - +
95A ASP* 2.9 46.7 + - - +
96A LEU 3.6 2.6 + - - -
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Residues in contact with TYR 93 (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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19A ARG* 3.9 38.6 + - - +
20A PRO 4.2 11.8 + - - -
22A LEU* 3.5 28.9 - - + -
84A THR* 3.9 26.5 - - + -
92A SER* 1.3 72.6 - - - +
94A GLU* 1.3 60.6 + - + +
96A LEU* 2.9 9.3 + - - +
97A ARG* 2.9 26.7 + - - +
109A MET* 4.1 16.7 - - + +
111A ASP* 5.1 0.3 + - - -
118A GLN* 4.1 13.2 - - - +
121A ASP* 2.7 38.4 + - + +
125A LEU* 3.6 22.5 - - + +
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Residues in contact with GLU 94 (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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22A LEU* 5.4 3.3 - - - +
92A SER* 3.0 12.6 - - - +
93A TYR* 1.3 79.0 - - + +
95A ASP* 1.3 69.7 + - - +
96A LEU 2.9 1.5 + - - -
97A ARG* 2.9 47.3 + - - +
98A LYS* 2.8 53.6 + - - +
125A LEU* 5.5 0.2 - - - +
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Residues in contact with ASP 95 (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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52A TYR* 4.0 12.6 - - + -
54A ARG* 2.9 42.9 + - - -
66A PRO* 3.5 14.9 - - + +
82A ILE* 3.9 17.7 - - + -
83A LEU 4.4 1.4 - - - +
91A GLY* 3.7 3.5 - - - -
92A SER* 2.9 35.6 + - - +
94A GLU* 1.3 77.3 - - - +
96A LEU* 1.3 63.2 + - - +
98A LYS* 4.0 4.0 - - - +
99A ILE* 3.1 31.2 + - + +
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Residues in contact with LEU 96 (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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82A ILE* 4.1 12.9 - - + +
84A THR* 4.3 14.8 - - + -
92A SER 3.6 1.4 + - - -
93A TYR 2.9 13.5 + - - +
94A GLU 2.9 0.6 - - - -
95A ASP* 1.3 79.7 - - - +
97A ARG* 1.3 54.1 - - - +
99A ILE* 3.7 0.7 - - - +
100A ALA* 2.7 42.8 + - + +
107A ILE* 3.6 31.0 - - + -
109A MET* 3.7 32.3 - - + -
122A ALA 4.5 0.7 - - - +
125A LEU* 3.8 24.9 - - + +
127A ALA* 3.8 25.1 - - + +
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Residues in contact with ARG 97 (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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22A LEU* 4.6 10.3 - - - +
23A ARG 4.8 4.2 + - - -
24A ALA* 4.5 17.6 - - - +
93A TYR 2.9 8.4 + - - +
94A GLU* 2.9 46.0 + - - +
96A LEU* 1.3 75.9 - - - +
98A LYS* 1.3 56.4 + - + +
100A ALA* 3.7 1.4 - - - +
101A SER* 2.8 36.2 + - - +
125A LEU* 3.8 41.7 + - + +
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Residues in contact with LYS 98 (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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65A ASP* 6.0 0.7 - - - +
66A PRO* 4.8 15.3 - - + -
67A ILE* 3.9 27.9 - - + +
94A GLU* 2.8 57.0 + - - +
95A ASP* 4.0 4.7 - - - +
97A ARG* 1.3 72.9 - - + +
99A ILE* 1.3 65.1 + - + +
101A SER* 3.1 17.5 + - - -
102A SER* 3.1 17.8 + - - -
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Residues in contact with ILE 99 (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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52A TYR* 4.6 9.0 - - + -
66A PRO* 3.7 44.0 - - + +
67A ILE* 4.1 1.6 - - - +
69A TYR* 5.6 0.7 - - + -
70A ALA* 3.4 23.1 - - + +
80A LEU* 4.2 3.8 - - + -
82A ILE* 3.7 39.0 - - + -
95A ASP* 3.1 20.0 + - + +
96A LEU 3.9 1.6 - - - +
98A LYS* 1.3 79.1 - - - +
100A ALA* 1.3 62.9 + - - +
102A SER* 3.1 16.1 + - - -
103A VAL* 3.2 23.3 + - + +
107A ILE* 4.4 7.4 - - + -
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Residues in contact with ALA 100 (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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28A ARG* 3.1 48.4 + - - +
96A LEU* 2.7 30.6 + - + +
97A ARG 3.7 1.6 - - - +
99A ILE* 1.3 74.9 - - - +
101A SER* 1.3 58.6 + - - +
102A SER 3.2 1.6 + - - -
103A VAL 3.4 1.9 - - - +
107A ILE* 4.8 4.9 - - + -
125A LEU 3.5 22.0 - - - +
126A GLY* 4.0 7.0 - - - +
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Residues in contact with SER 101 (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 ARG* 2.8 22.1 + - - +
98A LYS* 3.1 10.1 + - - -
100A ALA* 1.3 76.2 - - - +
102A SER* 1.3 58.5 + - - +
103A VAL 5.1 0.2 - - - -
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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