Contacts of the strand formed by residues 55 - 61 (chain S) in PDB entry 6D84
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 55 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3S HIS* 3.5 40.4 - - + +
4S PHE* 3.8 30.5 - - + -
21S ILE* 6.1 2.0 - - + -
50S VAL 3.1 0.2 - - - +
51S ASP* 3.4 5.0 + - - -
52S TRP* 2.9 48.8 + - + +
53S LYS* 3.1 18.9 - - - +
54S GLU* 1.3 83.8 - - + +
56S LYS* 1.3 61.1 + - - +
57S LEU* 2.9 8.0 + - + +
70S ALA* 3.9 12.6 - - + -
71S ILE 3.8 10.3 - - - +
72S GLU* 4.8 2.5 - - - -
73S ASN* 4.6 0.4 - - - -
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Residues in contact with LYS 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326G TYR* 3.3 23.8 - - + +
330G THR* 3.8 26.4 - - + +
333G LEU* 5.7 1.6 - - - +
364G ARG* 3.4 32.9 - - - +
49S PHE* 5.7 1.6 - - + -
50S VAL 3.4 4.9 - - - -
51S ASP* 4.5 1.1 - - - +
55S LEU* 1.3 68.3 - - - +
57S LEU* 1.3 63.4 + - - +
58S VAL* 3.5 4.0 + - - +
71S ILE* 4.0 14.4 + - + +
73S ASN* 3.3 44.2 + - + +
75S ASP 5.4 1.3 - - - +
77S GLU* 3.2 48.2 - - + +
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Residues in contact with LEU 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4S PHE* 4.1 16.2 - - + -
35S ILE* 4.3 11.9 - - + -
38S ILE* 6.4 2.0 - - + -
39S ILE* 4.0 7.6 - - + -
48S SER 3.8 0.5 - - - +
49S PHE* 3.6 9.4 - - - -
50S VAL* 2.5 45.9 + - + +
52S TRP* 4.3 24.7 - - + -
55S LEU* 2.9 7.5 + - + +
56S LYS* 1.3 72.0 - - - +
58S VAL* 1.3 62.8 + - - +
59S TYR* 3.7 26.7 - - + -
68S CYS* 3.7 28.3 - - - -
69S CYS 3.3 13.5 - - - +
70S ALA* 4.1 8.1 - - + -
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Residues in contact with VAL 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48S SER 4.2 4.5 - - - +
49S PHE* 4.2 10.1 - - + -
56S LYS 3.5 3.1 + - - +
57S LEU* 1.3 73.9 - - - +
59S TYR* 1.3 68.3 + - - +
60S LYS* 6.1 0.7 - - + -
68S CYS* 3.8 0.2 - - - -
69S CYS* 2.8 39.7 + - - +
70S ALA* 4.2 0.4 - - - +
71S ILE* 4.6 3.1 - - + +
77S GLU* 3.5 33.0 - - - +
80S THR* 3.7 42.8 - - + +
81S LEU* 4.0 20.0 - - + +
84S VAL* 5.4 5.8 - - + +
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Residues in contact with TYR 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39S ILE* 3.6 46.2 - - + -
42S ARG* 3.3 15.8 - - + +
43S GLY 4.7 4.7 + - - -
46S THR* 3.2 23.2 + - - -
48S SER* 3.2 56.8 + - - +
49S PHE 4.0 0.2 - - - -
50S VAL* 3.7 20.2 - - + -
57S LEU* 3.7 18.6 - - + -
58S VAL* 1.3 81.4 - - - +
60S LYS* 1.3 74.0 + - - +
61S ARG* 4.7 4.7 - - + -
66S TYR* 5.8 2.2 - + + -
67S PHE 3.2 16.4 - - - +
68S CYS* 4.2 1.1 - - - -
81S LEU* 5.2 2.4 - - - +
84S VAL* 6.5 0.7 - - - -
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Residues in contact with LYS 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48S SER* 4.1 13.9 - - - +
58S VAL* 6.1 0.7 - - + -
59S TYR* 1.3 87.4 - - - +
61S ARG* 1.3 87.7 + - - +
62S TYR* 3.6 42.3 + - + +
66S TYR* 4.1 2.2 - - - -
67S PHE* 3.1 31.8 + - - +
81S LEU* 4.3 29.2 - - + -
84S VAL* 5.0 8.1 - - + -
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Residues in contact with ARG 61 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S ARG* 5.8 0.4 - - - +
44S HIS* 4.3 26.5 + - - -
48S SER* 4.9 2.0 + - - -
59S TYR* 4.7 6.6 - - + -
60S LYS* 1.3 102.0 + - - +
62S TYR* 1.3 59.3 + - - +
63S ALA* 3.3 31.2 + - - +
64S SER* 4.9 3.0 - - - +
66S TYR* 3.5 36.7 + - + -
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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