Contacts of the helix formed by residues 51 - 61 (chain A) in PDB entry 6W01
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 PRO 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A THR 4.6 1.1 - - - +
50A LEU* 1.3 95.4 - - + +
52A VAL* 1.3 68.2 + - + +
53A ASN* 3.3 15.5 - - - +
54A VAL* 3.0 19.7 + - + +
55A ALA* 2.9 21.1 + - - +
105A MET* 5.5 8.7 - - + -
49B THR* 6.1 5.8 - - + +
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Residues in contact with VAL 52 (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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27A ILE* 3.6 26.7 - - + -
29A ASN 4.1 7.2 - - - +
30A ASN* 3.5 43.2 + - - +
31A THR 3.9 3.1 - - - +
32A VAL* 3.7 22.2 - - + -
44A PHE* 4.1 2.4 - - + -
46A ASN* 3.5 16.6 - - + +
50A LEU 3.5 1.8 + - - -
51A PRO* 1.3 71.8 - - - +
53A ASN* 1.3 68.7 + - - +
55A ALA* 3.6 1.4 + - - +
56A PHE* 3.0 22.5 + - - +
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Residues in contact with ASN 53 (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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3A LEU* 4.3 17.9 - - + +
27A ILE* 4.0 23.6 - - + -
32A VAL* 5.2 0.4 - - - -
51A PRO* 3.7 15.8 - - - +
52A VAL* 1.3 82.4 + - + +
54A VAL* 1.3 74.0 + - - +
56A PHE* 3.6 9.0 - - - +
57A GLU* 3.3 22.2 + - - +
105A MET* 5.5 3.2 - - - +
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Residues in contact with VAL 54 (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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50A LEU* 4.5 10.1 - - + -
51A PRO* 3.0 26.2 + - + +
53A ASN* 1.3 90.2 - - - +
55A ALA* 1.3 65.7 + - - +
57A GLU* 3.1 8.1 + - - +
58A LEU* 3.0 27.9 + - + +
103A CYS* 4.4 6.3 - - - -
105A MET* 3.8 34.8 - - + -
106A THR* 3.6 30.7 - - + -
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Residues in contact with ALA 55 (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 PHE* 3.8 10.0 - - + -
46A ASN* 3.2 29.6 - - - +
48A THR* 3.4 19.7 - - + +
50A LEU* 4.3 8.9 - - + +
51A PRO 2.9 13.9 + - - +
52A VAL 3.9 0.4 - - - +
54A VAL* 1.3 76.3 - - - +
56A PHE* 1.3 63.1 + - - +
58A LEU* 3.4 6.8 + - - +
59A TRP* 2.9 26.2 + - - +
87A TRP* 4.1 3.6 - - - -
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Residues in contact with PHE 56 (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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3A LEU* 3.7 28.9 - - + -
6A VAL* 3.6 17.7 - - + -
7A ALA* 3.8 32.1 - - + -
10A VAL* 4.0 12.8 - - + -
32A VAL* 4.0 15.5 - - + -
43A LEU* 4.1 17.5 - - + -
44A PHE* 3.4 42.5 - + + -
52A VAL 3.0 19.4 + - - +
53A ASN* 3.6 5.4 - - - +
54A VAL 3.2 0.2 - - - -
55A ALA* 1.3 76.5 - - - +
57A GLU* 1.3 58.0 + - + +
59A TRP* 3.5 18.0 + + - +
60A ALA* 3.0 26.5 + - - +
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Residues in contact with GLU 57 (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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1A MET* 3.2 22.3 - - - +
2A SER 5.4 2.1 - - - +
3A LEU* 5.9 0.9 - - - -
6A VAL* 4.1 20.8 - - + +
53A ASN 3.3 11.1 + - - +
54A VAL* 3.1 10.3 + - - +
56A PHE* 1.3 80.3 - - + +
58A LEU* 1.3 63.7 + - - +
60A ALA* 3.3 1.9 + - - +
61A LYS* 2.7 59.1 + - + +
103A CYS* 3.8 31.6 - - + -
104A SER 4.6 1.6 + - - -
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Residues in contact with LEU 58 (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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50A LEU* 3.7 31.0 - - + -
54A VAL* 3.0 19.0 + - + +
55A ALA 3.9 3.1 - - - +
57A GLU* 1.3 75.8 - - - +
59A TRP* 1.3 62.3 + - - +
61A LYS* 3.2 4.5 + - - -
62A ARG* 3.2 16.6 + - - -
85A VAL* 3.7 25.8 - - + +
87A TRP* 4.2 2.2 - - - -
94A PRO* 3.7 23.3 - - + -
96A HIS 5.6 0.4 - - - +
97A ILE 5.4 2.5 - - - +
99A THR* 4.0 17.9 - - + -
102A VAL* 4.1 2.7 - - + -
103A CYS* 3.7 18.6 - - + -
106A THR* 3.7 34.1 - - + +
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Residues in contact with TRP 59 (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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10A VAL* 4.1 22.9 - - + -
14A GLY 5.5 2.5 - - - -
43A LEU 3.9 15.9 - - - -
44A PHE* 3.6 21.5 - + + -
55A ALA 2.9 17.9 + - - +
56A PHE* 3.8 22.2 - + - +
58A LEU* 1.3 73.4 - - - +
60A ALA* 1.3 76.6 + - - +
62A ARG* 2.9 67.5 + - - +
87A TRP* 3.6 44.7 - + + +
89A TYR* 4.9 5.5 + - - -
401A EDO 3.5 32.5 - - - -
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Residues in contact with ALA 60 (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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6A VAL* 3.6 26.0 - - + -
10A VAL* 3.7 20.0 - - + -
15A HIS* 3.6 10.8 + - - +
16A PHE* 2.8 35.1 + - + +
56A PHE 3.0 17.5 + - - +
57A GLU 3.3 2.7 + - - +
59A TRP* 1.3 80.9 - - + +
61A LYS* 1.3 56.5 + - - +
62A ARG* 3.3 10.2 + - - +
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Residues in contact with LYS 61 (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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1A MET* 3.1 32.3 - - - +
16A PHE* 3.7 41.1 - - + -
57A GLU* 2.7 52.5 + - + +
58A LEU 3.2 6.9 + - - +
59A TRP 3.2 0.4 - - - -
60A ALA* 1.3 73.8 - - + +
62A ARG* 1.3 65.0 + - - +
63A ASN 3.7 0.3 + - - -
84A THR* 4.6 3.1 + - - -
85A VAL* 3.8 13.5 + - + +
102A VAL* 2.9 44.3 + - + +
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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