Contacts of the strand formed by residues 59 - 67 (chain S) in PDB entry 1C0F
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 59 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S GLY 3.2 24.0 - - - +
15S LYS* 3.6 17.3 - - - +
17S PRO* 4.0 24.2 - - + -
51S THR* 3.6 24.2 - - + -
52S VAL 3.4 2.0 - - - -
53S GLN* 4.0 24.9 - - - +
54S LEU* 3.8 2.0 - - - -
57S GLY 4.5 3.6 - - - +
58S ASN* 1.3 84.8 + - - +
60S GLN* 1.3 58.0 + - - +
61S TYR* 3.7 15.3 - - + +
93S ARG* 2.8 30.0 + - - -
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Residues in contact with GLN 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50S LYS* 3.5 1.8 + - - +
51S THR* 3.3 6.8 - - - -
52S VAL* 2.8 67.0 + - + +
54S LEU* 3.7 28.5 - - + +
59S LEU* 1.3 72.3 - - - +
61S TYR* 1.3 64.1 + - - +
62S ASP* 3.7 20.3 + - - +
93S ARG* 5.1 0.7 - - - +
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Residues in contact with TYR 61 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14S GLY* 2.9 42.6 + - - -
49S LEU* 3.8 13.7 - - + -
50S LYS 3.6 1.6 - - - -
51S THR* 3.7 22.2 - - + -
58S ASN* 4.8 1.6 + - - -
59S LEU* 3.7 19.5 - - + +
60S GLN* 1.3 82.0 - - - +
62S ASP* 1.3 67.5 + - - +
90S LEU* 4.1 31.4 - - + +
93S ARG* 3.2 48.6 + - + +
94S ALA* 3.4 19.5 - - + -
95S VAL* 2.9 24.4 + - - +
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Residues in contact with ASP 62 (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 ILE 3.7 1.0 - - - +
49S LEU* 3.5 3.8 - - - +
50S LYS* 3.0 38.3 + - + +
60S GLN* 3.7 23.7 + - - +
61S TYR* 1.3 78.1 - - - +
63S LEU* 1.3 63.4 + - - +
64S HIS* 3.6 20.1 - - - +
95S VAL* 3.5 14.8 - - - +
97S HIS* 2.7 25.3 + - - +
107S THR* 6.1 2.2 - - - -
111S TYR* 3.7 10.1 - - - +
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Residues in contact with LEU 63 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S VAL* 4.1 12.3 - - + -
48S ILE 3.4 5.8 - - - +
49S LEU* 3.8 31.9 - - + -
61S TYR 4.1 0.4 - - - -
62S ASP* 1.3 74.1 - - - +
64S HIS* 1.3 61.1 + - - +
83S THR* 3.5 39.3 - - + +
86S LEU* 3.9 25.1 - - + -
87S ASP* 3.6 19.5 - - + +
90S LEU* 5.1 1.1 - - + -
94S ALA* 3.6 22.2 - - + -
95S VAL 2.8 12.4 + - - +
96S GLN* 3.4 2.1 - - + +
97S HIS* 2.7 28.6 + - - -
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Residues in contact with HIS 64 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S VAL* 3.4 1.9 - - - +
48S ILE* 2.7 48.8 + - - +
62S ASP* 3.6 13.1 - - - +
63S LEU* 1.3 81.0 - - - +
65S TYR* 1.3 60.6 + - - +
66S TRP 4.0 0.2 - - - -
83S THR* 4.8 2.2 - - - -
97S HIS* 3.3 33.6 - + - +
99S GLU* 2.9 28.6 + - + -
105S SER* 4.5 3.8 - - - -
107S THR* 4.8 4.9 - - + -
108S PHE* 3.6 34.0 - + + -
111S TYR* 2.7 43.3 + + - -
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Residues in contact with TYR 65 (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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146A GLY 3.4 22.2 - - - -
147A ARG* 3.6 2.9 - - - -
148A THR* 3.1 45.2 + - + -
149A THR 4.7 0.7 + - - -
46S TYR 3.2 9.9 - - - +
47S VAL* 4.7 1.1 - - + -
64S HIS* 1.3 71.6 - - - +
66S TRP* 1.3 56.8 + - - +
67S LEU* 4.0 13.1 + - + +
79S ALA* 3.8 13.2 - - + +
80S ALA* 4.0 19.1 - - + -
83S THR* 3.5 33.4 - - + +
96S GLN* 4.9 1.1 - - + -
97S HIS 3.0 29.3 + - - -
98S ARG* 3.5 26.6 - - + +
99S GLU* 2.7 34.3 + - - +
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Residues in contact with TRP 66 (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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40S PHE* 3.6 30.7 - + + -
41S PHE 3.5 23.1 - - - -
42S THR* 4.1 4.5 - - + -
44S ASP 3.5 2.2 - - - -
45S ALA* 3.2 7.1 - - - +
46S TYR* 2.8 54.6 + + + +
48S ILE* 3.9 20.4 - - + -
64S HIS 4.0 0.8 + - - -
65S TYR* 1.3 72.3 - - - +
67S LEU* 1.3 61.6 + - - +
68S GLY* 3.5 24.9 - - - -
99S GLU* 3.3 19.5 - - + -
101S GLN* 4.0 23.6 - - + +
104S GLU* 3.0 22.0 + - + -
108S PHE* 3.6 27.3 - + + -
116S LEU* 5.0 1.2 - - - +
118S TYR* 3.8 23.1 - + - -
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Residues in contact with LEU 67 (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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146A GLY* 3.8 11.4 - - - +
44S ASP 4.4 0.2 - - - -
45S ALA* 3.8 9.0 - - + -
65S TYR* 4.4 11.2 - - + +
66S TRP* 1.3 83.7 - - - +
68S GLY* 1.3 62.9 - - - +
69S ASN* 4.9 0.2 - - - -
71S CYS* 4.4 7.6 - - - -
76S SER* 3.5 41.7 - - - +
79S ALA* 4.2 8.1 - - + -
98S ARG* 3.7 38.4 - - + +
99S GLU 2.8 16.9 + - - +
100S VAL* 4.0 8.6 - - + +
101S GLN* 3.1 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