Contacts of the helix formed by residues 83 - 98 (chain A) in PDB entry 2UYK
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 83 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL* 3.7 31.3 - - + +
78A ILE* 6.1 0.2 - - - +
79A THR* 4.9 0.7 + - - -
80A ASP* 2.9 37.4 + - - +
82A ASN* 1.3 76.2 - - - +
84A PHE* 1.3 64.3 + - - +
85A ALA 3.3 1.8 - - - -
86A THR* 3.2 9.6 + - - -
87A ILE* 3.0 36.3 + - + +
118A LYS* 4.0 19.3 + - - +
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Residues in contact with PHE 84 (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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76A VAL* 5.9 1.3 - - + -
78A ILE* 4.5 5.2 - - + -
80A ASP 4.1 0.6 + - - -
81A LEU* 3.0 32.5 + - + +
82A ASN 3.2 0.6 - - - -
83A ASP* 1.3 77.9 - - - +
85A ALA* 1.3 56.5 + - - +
87A ILE* 4.3 14.8 - - + -
88A ASN* 2.7 63.5 + - + +
105A ARG* 3.4 35.0 - - - -
107A CYS* 3.7 34.3 - - + -
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASN 4.5 5.6 + - - +
83A ASP 3.3 1.0 - - - -
84A PHE* 1.3 80.6 - - - +
86A THR* 1.3 63.2 + - - +
88A ASN* 3.7 5.5 - - - +
89A GLU* 3.0 24.4 + - - +
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Residues in contact with THR 86 (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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46A VAL* 4.0 14.7 - - + +
47A GLN* 3.9 41.7 - - + +
83A ASP* 3.2 10.3 + - - -
85A ALA* 1.3 76.6 - - - +
87A ILE* 1.3 69.3 + - - +
89A GLU* 3.3 6.9 + - - +
90A VAL* 3.1 22.7 + - - +
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Residues in contact with ILE 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 4.0 19.7 - - + +
50A ALA* 4.2 19.4 - - + +
54A LEU* 5.5 0.8 - - + +
76A VAL* 4.8 11.9 - - + -
78A ILE* 4.0 30.1 - - + -
83A ASP* 3.0 36.8 + - + +
84A PHE* 3.7 13.7 - - + +
86A THR* 1.3 75.6 - - - +
88A ASN* 1.3 59.3 + - - +
90A VAL* 3.2 4.0 + - - +
91A TYR* 2.8 35.3 + - + +
105A ARG* 6.1 0.4 - - - +
118A LYS 5.0 2.0 - - - +
119A LEU* 4.2 23.8 - - + -
121A ILE* 5.9 1.3 - - + -
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Residues in contact with ASN 88 (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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84A PHE* 2.7 47.4 + - + +
85A ALA* 3.7 5.4 - - - +
87A ILE* 1.3 74.5 - - - +
89A GLU* 1.3 57.9 + - - +
91A TYR* 3.5 4.7 - - - +
92A LYS* 2.8 31.8 + - - +
105A ARG* 2.9 29.2 + - - +
14B ILE 5.4 1.4 + - - -
15B GLY* 4.9 3.4 - - - -
16B PRO* 3.1 26.6 - - - +
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Residues in contact with GLU 89 (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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85A ALA 3.0 17.6 + - - +
86A THR* 3.8 6.5 - - - +
87A ILE 3.2 0.2 - - - -
88A ASN* 1.3 74.2 - - - +
90A VAL* 1.3 65.6 + - + +
92A LYS* 3.7 22.0 - - - +
93A GLN* 3.0 69.0 + - - +
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Residues in contact with VAL 90 (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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47A GLN* 3.6 40.8 - - + +
50A ALA* 4.0 9.4 - - + -
51A ARG* 3.6 45.1 + - + +
54A LEU* 4.0 7.0 - - + -
86A THR 3.1 14.5 + - - +
87A ILE 3.6 6.5 - - - +
89A GLU* 1.3 75.9 - - + +
91A TYR* 1.3 58.0 + - - +
93A GLN* 3.3 8.4 + - - +
94A PHE* 2.9 27.4 + - - +
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Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.8 26.7 - - + -
74A MET* 3.1 41.1 - - - +
76A VAL* 4.0 13.5 - - + -
87A ILE* 2.8 24.1 + - + +
88A ASN* 3.5 8.7 - - - +
90A VAL* 1.3 75.4 - - - +
92A LYS* 1.3 65.7 + - - +
94A PHE* 3.3 2.1 + - - +
95A PHE* 3.2 50.8 + + - -
103A PRO* 3.7 9.1 - - + +
105A ARG* 3.4 41.4 - - - +
121A ILE* 5.0 3.1 - - + -
16B PRO* 3.3 29.3 + - + -
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Residues in contact with LYS 92 (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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88A ASN 2.8 21.0 + - - +
89A GLU* 3.7 22.9 - - - +
91A TYR* 1.3 74.2 - - - +
93A GLN* 1.3 58.5 + - + +
95A PHE* 3.4 1.9 + - - +
96A ASP* 2.7 62.1 + - - +
102A TYR* 2.9 22.3 + - + +
15B GLY* 5.8 2.0 - - - -
16B PRO* 3.8 27.4 - - + -
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Residues in contact with GLN 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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51A ARG* 5.5 2.2 - - - +
89A GLU* 3.0 54.8 + - - +
90A VAL* 3.7 7.8 - - - +
92A LYS* 1.3 76.2 - - + +
94A PHE* 1.3 53.9 + - - +
96A ASP* 3.7 7.0 - - - +
97A GLU* 2.8 54.1 + - + +
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Residues in contact with PHE 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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51A ARG* 3.9 18.6 - - - +
54A LEU* 3.6 56.1 - - + -
55A GLU* 3.6 26.0 - - - -
57A VAL* 5.6 1.1 - - + -
58A LYS* 4.0 7.4 - - + -
68A VAL* 3.5 37.0 - - + -
71A ILE* 5.1 4.9 - - + -
90A VAL 2.9 17.1 + - - +
91A TYR 3.4 4.0 - - - +
92A LYS 3.2 0.4 - - - -
93A GLN* 1.3 76.7 - - - +
95A PHE* 1.3 84.7 + + - +
97A GLU* 3.5 2.0 + - - +
98A HIS* 2.9 44.6 + + - -
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Residues in contact with PHE 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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54A LEU* 4.8 0.2 - - + -
68A VAL* 3.6 32.8 - - + -
71A ILE* 4.4 7.0 - - + -
74A MET* 3.7 17.7 - - + -
91A TYR* 3.2 55.4 + + - +
94A PHE* 1.3 96.3 - + - +
96A ASP* 1.3 63.4 + - - +
98A HIS 3.1 3.5 + - - -
99A GLN 3.1 4.0 + - - -
100A ALA* 3.0 39.2 + - + +
101A THR 4.0 4.9 - - - -
102A TYR* 3.7 24.7 - + + -
103A PRO* 3.5 32.1 - - + -
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Residues in contact with ASP 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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92A LYS* 2.7 47.2 + - - +
93A GLN* 3.9 6.6 + - - +
95A PHE* 1.3 77.0 - - - +
97A GLU* 1.3 62.2 + - + +
99A GLN* 3.0 20.6 + - - +
100A ALA 5.0 2.1 - - - +
102A TYR* 2.5 28.0 + - - -
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Residues in contact with GLU 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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51A ARG* 3.1 37.2 + - - -
93A GLN* 2.8 40.9 + - + +
94A PHE 3.8 4.9 - - - +
95A PHE 3.3 0.2 - - - -
96A ASP* 1.3 73.2 - - - +
98A HIS* 1.3 68.9 + - + +
99A GLN* 3.3 9.1 + - - +
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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
----------------------------------------------------------
51A ARG* 4.9 1.8 - - - -
55A GLU* 4.8 2.9 - - - -
58A LYS* 3.8 23.5 + - + +
67A SER* 6.4 0.9 - - - -
68A VAL* 3.9 33.6 - - + +
69A GLY* 5.2 3.4 + - - +
94A PHE* 2.9 48.1 + + - +
95A PHE 3.1 4.4 + - - +
97A GLU* 1.3 89.5 - - + +
99A GLN* 1.3 70.8 + - - +
100A ALA* 3.1 5.3 + - + +
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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