Contacts of the helix formed by residues 82 - 94 (chain A) in PDB entry 6RKU
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 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A VAL* 4.5 8.2 - - + +
74A ILE* 3.6 20.4 - - + -
80A HIS 4.0 0.2 + - - -
81A GLY* 1.3 76.2 - - - -
83A SER* 1.3 86.7 + - - +
84A ALA 3.3 2.5 - - - -
85A VAL* 3.2 6.0 + - - +
86A TYR* 2.9 26.1 + - - +
120A MET* 4.9 6.3 - - + -
101G JHN 3.1 47.1 + - + +
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASP* 1.3 87.9 + - - +
84A ALA* 1.3 62.3 + - - +
86A TYR* 3.9 4.5 - - - +
87A ASP* 2.9 42.1 + - - +
120A MET* 5.7 2.2 - - - -
13E A 5.9 1.0 + - - -
14E G 5.4 5.5 + - - -
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 5.9 0.4 - - - -
80A HIS 4.8 8.9 + - - +
82A ASP 3.3 0.8 - - - +
83A SER* 1.3 83.1 + - - +
85A VAL* 1.3 60.2 + - + +
87A ASP* 3.8 6.8 - - - +
88A THR* 2.9 34.0 + - - -
12E T 3.9 20.8 - - + +
13E A 3.9 37.2 - - + +
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Residues in contact with VAL 85 (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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44A VAL* 5.0 7.4 - - + -
48A VAL* 4.5 9.9 - - + -
70A VAL* 4.9 13.2 - - + +
73A VAL* 4.4 24.5 - - + -
74A ILE* 5.0 3.4 - - + -
78A HIS* 3.8 33.0 - - + +
80A HIS 5.3 0.4 - - - +
81A GLY 4.0 15.5 - - - +
82A ASP* 3.2 9.0 + - - +
84A ALA* 1.3 76.2 - - + +
86A TYR* 1.3 58.8 - - - +
88A THR* 3.2 7.8 + - - -
89A ILE* 3.0 43.0 + - + +
13E A 5.4 0.2 - - - +
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Residues in contact with TYR 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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66A SER* 4.4 12.3 - - - -
70A VAL* 4.4 16.1 - - + +
82A ASP 2.9 16.5 + - - +
83A SER* 4.0 3.6 - - - +
85A VAL* 1.3 77.6 - - - +
87A ASP* 1.3 67.0 + - - +
89A ILE* 3.3 13.2 + - + +
90A VAL* 2.9 58.9 + - + +
109A PHE* 5.5 0.2 - - - -
117A ALA* 4.7 3.0 - - + +
118A ALA 3.0 26.7 + - - -
119A ALA* 3.3 9.5 + - - -
120A MET* 3.5 50.2 - - + -
123A THR* 3.9 16.0 - - - +
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A SER* 2.9 29.7 + - - +
84A ALA* 3.8 6.9 + - - +
86A TYR* 1.3 85.2 - - - +
88A THR* 1.3 58.2 + - - +
90A VAL* 3.3 7.0 + - - +
91A ARG* 2.9 29.5 + - - +
12E T 5.5 11.0 - - + +
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Residues in contact with THR 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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44A VAL* 4.1 21.6 - - + +
45A HIS* 3.4 39.5 - - + +
48A VAL* 5.7 2.7 - - + -
84A ALA 2.9 19.1 + - - -
85A VAL 3.2 5.6 + - - -
87A ASP* 1.3 77.5 - - - +
89A ILE* 1.3 62.3 + - + +
91A ARG* 3.4 14.4 + - + +
92A MET* 3.4 19.3 + - + +
12E T 3.6 28.0 + - - +
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Residues in contact with ILE 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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48A VAL* 4.4 25.6 - - + -
52A MET* 4.9 2.7 - - + -
66A SER* 5.8 2.9 - - - +
69A VAL* 4.7 12.1 - - + -
70A VAL* 4.1 21.5 - - + -
73A VAL* 6.1 0.4 - - + -
85A VAL* 3.0 35.2 + - + +
86A TYR* 3.6 12.8 - - + +
87A ASP 3.3 0.2 - - - -
88A THR* 1.3 78.1 - - - +
90A VAL* 1.3 64.3 + - + +
92A MET* 3.2 22.1 + - + +
93A ALA* 3.5 11.5 + - + +
103A VAL* 4.8 9.1 - - + +
125A ILE* 4.4 30.3 - - + -
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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
----------------------------------------------------------
86A TYR* 2.9 57.7 + - + +
87A ASP* 3.8 6.7 - - - +
89A ILE* 1.3 77.2 - - + +
91A ARG* 1.3 63.4 + - - +
93A ALA* 3.2 15.9 + - - +
94A GLN* 3.6 27.4 + - - +
109A PHE* 4.4 16.2 - - + +
117A ALA* 3.8 25.4 - - + -
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Residues in contact with ARG 91 (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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45A HIS* 5.2 6.7 + - - -
87A ASP 2.9 17.3 + - - +
88A THR* 3.6 7.9 - - - +
89A ILE 3.2 0.4 - - - -
90A VAL* 1.3 79.7 - - - +
92A MET* 1.3 71.9 + - - +
93A ALA 3.4 0.2 + - - -
94A GLN* 3.5 22.8 + - - +
97A SER* 3.8 26.4 + - - +
98A LEU* 4.1 22.6 - - - +
171A SER* 5.5 11.7 + - - +
172A SER* 5.8 1.8 - - - +
266A TYR* 5.5 3.8 + - - -
267A GLN* 5.6 3.4 - - - +
11E G 3.8 38.9 + - - +
12E T 3.6 26.3 + - - +
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Residues in contact with MET 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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45A HIS* 3.4 36.6 - - + +
48A VAL* 4.7 14.6 - - + -
49A LEU* 5.6 7.2 - - + -
88A THR* 3.4 21.9 + - + +
89A ILE* 3.2 22.8 + - + +
90A VAL 3.2 0.8 - - - -
91A ARG* 1.3 81.2 - - - +
93A ALA* 1.3 61.7 + - - +
94A GLN 3.5 1.2 + - - +
98A LEU* 3.7 25.0 - - + +
101A MET* 3.7 20.8 - - - +
102A LEU* 4.1 20.3 + - + -
103A VAL* 4.0 31.1 + - + +
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Residues in contact with ALA 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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89A ILE* 3.5 8.8 + - + +
90A VAL* 3.2 10.6 + - - +
92A MET* 1.3 77.4 - - - +
94A GLN* 1.3 64.2 + - - +
95A PRO* 3.3 10.4 - - - +
101A MET* 4.3 11.2 - - - +
103A VAL* 3.5 27.2 - - + +
105A GLY 4.9 0.7 + - - +
109A PHE* 3.5 39.8 - - + -
125A ILE* 6.0 0.7 - - + -
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Residues in contact with GLN 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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90A VAL* 3.6 24.0 - - - +
91A ARG* 3.5 12.5 + - - +
92A MET 3.3 7.3 - - - +
93A ALA* 1.3 76.4 - - - +
95A PRO* 1.3 71.3 - - + +
96A PHE* 3.3 36.9 - - + -
97A SER* 3.6 22.3 + - - -
98A LEU* 3.8 9.9 + - - +
101A MET* 4.8 1.8 - - - +
109A PHE* 3.1 31.3 + - + +
110A GLY* 4.9 2.6 - - - -
115A ASP 5.8 0.6 + - - -
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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