Contacts of the helix formed by residues 93 - 106 (chain A) in PDB entry 2UVQ
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 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A PHE* 2.7 21.3 + - - +
69A LYS* 3.6 20.0 - - + +
92A PHE* 1.3 67.7 - - - +
94A ASN* 1.3 61.0 + - - +
95A ASP* 3.5 8.8 + - - +
96A LEU* 3.2 28.6 + - + +
97A MET* 3.1 20.9 + - - +
122A ARG* 3.1 28.5 + - - +
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Residues in contact with ASN 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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64A GLN* 5.0 2.1 + - - -
69A LYS* 5.4 0.2 - - - +
89A PRO* 3.5 22.7 + - - +
90A ASP* 5.1 2.6 + - - +
92A PHE* 2.8 32.3 + - - +
93A ASP* 1.3 72.4 + - - +
95A ASP* 1.3 56.7 + - - +
97A MET* 3.6 24.1 - - + +
98A HIS* 2.8 31.7 + - - +
148A ILE* 4.8 4.6 - - + +
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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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93A ASP* 3.1 7.8 + - - +
94A ASN* 1.3 75.9 - - - +
96A LEU* 1.3 56.7 + - - +
98A HIS* 3.2 7.1 + - - +
99A ARG* 2.8 77.4 + - - +
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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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67A PHE* 3.8 15.3 - - + -
93A ASP* 3.2 22.0 + - - +
95A ASP* 1.3 78.6 + - - +
97A MET* 1.3 53.7 + - - +
99A ARG* 3.7 6.3 - - + +
100A THR* 2.7 44.8 + - - +
111A GLU 6.1 1.3 - - - +
113A PRO* 3.7 31.0 - - + -
122A ARG* 3.7 28.0 - - - +
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Residues in contact with MET 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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64A GLN* 3.6 44.2 - - - +
67A PHE* 3.7 35.6 - - + -
92A PHE* 5.3 2.9 - - - -
93A ASP 3.1 13.7 + - - +
94A ASN* 3.6 18.4 - - - +
96A LEU* 1.3 79.3 - - - +
98A HIS* 1.3 64.7 + - - +
100A THR* 3.1 3.8 + - - -
101A LEU* 3.1 25.4 + - - +
137A PHE* 3.9 25.1 - - + -
141A LEU 5.3 2.2 - - - +
142A VAL* 5.2 1.3 - - + -
145A SER* 5.3 0.2 - - - +
148A ILE* 3.1 37.0 - - + -
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Residues in contact with HIS 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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94A ASN 2.8 21.2 + - - +
95A ASP* 3.9 6.5 - - - +
97A MET* 1.3 72.6 - - - +
99A ARG* 1.3 65.6 + - + +
101A LEU* 3.6 5.1 + - - +
102A LYS* 2.9 52.8 + - + +
147A GLU* 4.0 35.9 + - + +
148A ILE* 3.9 30.2 - - + +
151A MET* 4.7 13.0 - - + +
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Residues in contact with ARG 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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95A ASP* 2.8 51.5 + - - +
96A LEU* 3.7 7.0 - - + +
98A HIS* 1.3 82.6 - - + +
100A THR* 1.3 68.1 + - - +
102A LYS* 3.3 15.0 + - + +
103A ASN* 3.0 30.5 + - - +
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Residues in contact with THR 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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62A LEU* 5.2 1.3 - - + -
67A PHE* 3.7 26.9 - - + -
96A LEU* 2.7 36.9 + - - +
97A MET 3.1 4.2 + - - -
99A ARG* 1.3 69.7 - - - +
101A LEU* 1.3 68.2 - - - +
103A ASN* 2.8 19.6 + - - +
104A ILE* 2.9 22.0 + - + +
110A VAL* 3.9 31.4 - - + -
111A GLU 5.1 5.5 + - - +
112A VAL* 4.3 8.5 - - + -
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Residues in contact with LEU 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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25A LEU* 3.3 40.2 - - + -
62A LEU* 3.7 18.6 - - + -
67A PHE* 5.9 0.4 - - + -
97A MET* 3.1 11.0 + - + +
98A HIS* 3.6 10.1 - - - +
100A THR* 1.3 77.9 - - - +
102A LYS* 1.3 56.5 - - - +
104A ILE* 3.1 10.5 + - + +
105A VAL* 2.8 34.6 + - - +
135A VAL* 6.1 0.7 - - + -
137A PHE* 3.4 46.9 - - + -
148A ILE* 5.1 8.5 - - + -
151A MET* 4.2 17.7 - - + -
152A PHE* 5.0 2.7 - - + -
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Residues in contact with LYS 102 (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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98A HIS* 2.9 43.5 + - + +
99A ARG* 3.5 15.7 - - + +
100A THR 3.0 0.2 + - - -
101A LEU* 1.3 76.1 - - - +
103A ASN* 1.3 60.0 + - - +
105A VAL* 3.6 4.2 - - + +
106A GLU* 3.0 53.8 + - + +
151A MET* 4.0 19.5 - - + -
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Residues in contact with ASN 103 (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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99A ARG* 3.0 24.0 + - - +
100A THR* 2.8 8.9 + - - +
102A LYS* 1.3 76.4 - - - +
104A ILE* 1.3 64.7 + - - +
105A VAL 3.2 0.2 - - - -
106A GLU* 3.0 24.8 + - - +
107A GLY 3.2 0.5 + - - -
108A LYS* 3.1 48.7 + - + +
110A VAL* 3.8 17.1 - - + +
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Residues in contact with ILE 104 (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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23A PRO* 3.5 14.1 - - + +
25A LEU* 4.6 8.7 - - + -
62A LEU* 3.8 31.6 - - + -
100A THR* 2.9 29.9 + - + +
101A LEU* 3.4 16.8 - - + +
103A ASN* 1.3 70.1 - - - +
105A VAL* 1.3 55.0 + - - +
107A GLY* 2.7 27.4 + - - -
108A LYS 4.2 9.6 - - - +
110A VAL* 3.9 22.6 - - + +
129A VAL* 5.5 7.6 - - + -
131A PRO* 6.0 1.7 - - + +
132A ALA 6.1 2.0 - - - +
135A VAL* 3.9 30.7 - - + -
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Residues in contact with VAL 105 (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 ARG 4.3 2.8 - - - +
23A PRO* 3.4 25.6 - - + +
25A LEU* 3.6 33.0 - - + -
101A LEU 2.8 16.0 + - - +
102A LYS* 3.6 8.5 - - + +
104A ILE* 1.3 72.6 - - - +
106A GLU* 1.3 64.1 + - + +
107A GLY 3.1 3.0 + - - -
151A MET* 3.6 30.1 - - + +
153A HIS* 6.1 1.3 - - - +
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Residues in contact with GLU 106 (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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102A LYS* 3.0 38.5 + - + +
103A ASN* 3.0 17.8 + - - +
105A VAL* 1.3 79.9 - - + +
107A GLY* 1.3 59.8 + - - +
108A LYS* 3.0 38.4 + - - +
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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