Contacts of the strand formed by residues 64 - 70 (chain C) in PDB entry 6P59
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 LEU 64 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C PHE* 4.2 14.8 - - + -
19C ARG 4.4 1.1 - - - +
20C LYS* 4.3 10.1 - - + +
21C LEU* 3.8 38.4 - - + -
58C VAL* 3.6 2.6 - - - +
59C ALA* 3.1 29.5 + - + +
62C THR* 3.0 13.4 + - - +
63C ASN* 1.3 80.3 + - - +
65C SER* 1.3 69.3 + - - +
66C LEU* 6.2 3.6 - - + -
10F PRO* 4.9 11.0 - - + -
11F VAL 4.1 5.4 - - - +
12F TRP* 3.6 50.0 - - + +
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Residues in contact with SER 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ALA* 4.6 4.9 - - - +
57C PHE 3.2 17.7 - - - -
58C VAL* 4.1 4.9 - - - -
64C LEU* 1.3 80.9 - - - +
66C LEU* 1.3 62.8 + - - +
67C GLN* 4.3 5.2 + - - +
10F PRO* 3.7 3.1 - - - +
11F VAL* 2.8 54.9 + - - +
13F ARG* 3.8 30.5 + - - +
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LEU* 6.2 3.4 - - + -
56C ALA* 3.6 0.3 - - - -
57C PHE* 3.0 34.1 + - + +
64C LEU* 6.2 4.0 - - + -
65C SER* 1.3 70.8 - - - +
67C GLN* 1.3 61.1 + - - +
68C PHE* 3.5 23.4 - - + -
99C ALA* 4.3 6.3 - - + -
101C MET* 3.6 36.3 - - + -
110C TRP* 3.6 50.7 - - + -
8F VAL* 4.6 4.5 - - + -
9F ARG 4.6 0.7 - - - +
10F PRO* 4.0 19.5 - - + -
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Residues in contact with GLN 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLU* 3.8 16.4 - - - +
55C ILE 3.2 27.2 + - - -
56C ALA* 3.4 18.7 - - - +
65C SER* 3.6 4.8 + - - +
66C LEU* 1.3 71.4 - - - +
68C PHE* 1.3 69.3 + - - +
69C PHE* 3.4 32.9 - - + -
7F ILE 3.8 1.0 - - - +
8F VAL* 3.4 6.4 - - - +
9F ARG 3.3 29.7 + - - +
11F VAL* 3.8 28.0 - - + +
13F ARG* 5.0 2.3 + - - -
76F LEU* 3.3 31.2 - - + +
77F THR* 5.2 0.7 + - - -
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Residues in contact with PHE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLU* 3.8 4.7 - - - -
55C ILE* 3.0 44.1 + - + +
57C PHE* 3.9 27.6 - + - -
66C LEU* 3.5 30.3 - - + -
67C GLN* 1.3 78.9 + - - +
69C PHE* 1.3 59.8 + - - +
85C TYR* 4.2 4.3 - - + -
86C VAL* 3.6 24.7 - - + -
97C LEU* 4.2 17.7 - - + -
98C LYS 3.6 23.8 - - - -
99C ALA* 4.3 6.5 - - + -
110C TRP* 5.3 1.1 - + - -
6F TRP* 3.8 21.1 - - + -
7F ILE 3.6 2.2 - - - -
8F VAL* 4.0 23.8 - - + -
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Residues in contact with PHE 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLU* 4.5 2.0 - - + -
67C GLN* 3.4 38.1 - - + -
68C PHE* 1.3 76.3 - - - +
70C PRO* 1.3 65.1 - - + +
74C GLN* 3.9 20.9 - - + -
6F TRP* 3.2 10.6 - - - -
7F ILE* 2.9 50.9 + - + -
9F ARG* 5.8 7.4 - - + -
11F VAL* 5.2 1.8 - - + -
53F TRP* 3.4 45.1 - + + -
73F TYR* 3.9 44.6 - + - -
76F LEU* 4.2 8.7 - - + -
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Residues in contact with PRO 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C GLY 3.6 17.7 - - - +
52C ARG* 3.9 7.4 - - - -
53C SER 3.1 41.3 - - - +
54C GLU* 4.6 0.2 - - - -
68C PHE 4.5 0.4 - - - +
69C PHE* 1.3 81.5 - - + +
71C ALA* 1.3 66.5 + - - +
72C SER* 3.2 4.0 - - - +
73C TRP* 3.0 16.6 + - + +
74C GLN* 3.3 11.6 + - - +
4F LYS* 4.3 8.3 - - + -
5F MET 3.9 6.7 - - - +
6F TRP* 4.3 3.3 - - + -
53F TRP* 3.5 23.6 - - + -
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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