Contacts of the strand formed by residues 68 - 76 (chain B) in PDB entry 1CF5
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 ASN 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 4.4 1.1 - - - +
65B ASP* 3.1 38.9 - - - +
66B VAL 3.3 0.6 + - - -
67B THR* 1.3 90.8 - - + +
69B VAL* 1.3 58.0 + - - +
70B TYR* 2.9 45.7 + - + +
161B ARG* 2.7 29.8 + - - -
190B TRP* 3.5 2.8 - - - -
239B LEU* 3.7 22.4 - - + -
240B ASN* 4.7 0.2 - - - +
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PHE* 3.3 36.6 - - + -
25B LEU* 4.1 13.0 - - + -
37B LEU* 3.8 22.0 - - + -
64B ILE* 3.9 7.6 - - + +
65B ASP 2.8 11.9 + - - -
66B VAL 4.3 1.0 - - - -
68B ASN* 1.3 80.4 - - - +
70B TYR* 1.3 60.9 + - - +
157B ALA* 3.1 33.8 - - + +
160B ALA* 4.7 0.2 - - + -
161B ARG* 3.8 18.7 + - - +
190B TRP* 4.4 2.5 - - + -
237B LEU* 3.8 20.4 - - + -
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Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 3.5 2.7 - - - -
65B ASP* 2.8 33.9 + - + +
68B ASN* 2.9 49.0 + - + +
69B VAL* 1.3 78.5 - - - +
71B VAL* 1.3 65.1 + - - +
72B VAL* 4.9 3.1 - - + -
108B ASN* 6.5 1.3 - - + -
153B ILE* 6.2 5.2 - - + -
161B ARG* 3.7 21.1 - - - -
190B TRP* 4.4 9.8 - + - -
239B LEU* 5.2 6.6 - - - +
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 4.1 13.2 - - + -
63B ALA 3.4 8.1 - - - +
64B ILE* 3.9 16.6 - - + -
70B TYR* 1.3 74.3 - - - +
72B VAL* 1.3 61.7 + - - +
73B ALA 3.8 22.9 - - - +
74B TYR* 5.7 0.4 - - + -
83B PHE* 3.5 28.1 - - + -
107B GLY* 5.4 1.6 - - - -
149B LEU* 5.4 4.5 - - + -
152B LEU* 5.1 11.0 - - + -
153B ILE* 4.2 33.6 - - + +
156B THR* 5.2 2.9 - - - +
157B ALA* 5.0 6.1 - - + -
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PHE* 3.6 33.4 - - + -
63B ALA* 2.9 24.1 + - + +
65B ASP* 3.8 20.6 - - + +
70B TYR* 4.3 4.0 - - + +
71B VAL* 1.3 76.0 - - - +
73B ALA* 1.3 64.9 + - + +
82B PHE* 3.8 1.2 - - - -
83B PHE* 3.3 18.3 + - - -
86B SER* 2.8 27.1 + - - +
87B PRO* 3.7 23.1 - - + -
90B ALA* 4.6 1.3 - - + -
94B LEU* 4.0 11.9 - - + -
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B VAL* 3.7 0.5 - - - -
63B ALA* 2.8 26.0 + - + +
71B VAL* 3.4 13.1 - - - +
72B VAL* 1.3 86.9 - - + +
74B TYR* 1.3 65.2 + - - +
81B TYR 3.0 18.8 - - - +
82B PHE* 3.8 25.4 - - + +
83B PHE* 4.4 4.7 - - - +
95B PHE* 4.1 13.5 - - + -
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Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ILE* 4.0 17.0 - - + -
61B SER 3.1 13.5 - - - +
62B VAL* 3.8 14.4 - - + -
71B VAL* 5.7 1.1 - - + -
73B ALA* 1.3 76.2 - - - +
75B ARG* 1.3 78.8 + - - +
76B THR* 4.0 15.5 - - + -
80B SER* 3.3 2.9 - - - -
81B TYR* 2.9 55.2 + + + +
95B PHE* 4.1 6.7 - - - -
103B LEU* 5.7 2.5 - - + -
137B LEU* 2.6 54.7 + - + +
140B TYR* 3.5 26.4 - + - +
145B ALA* 6.0 0.2 - - + -
149B LEU* 4.4 23.1 - - + -
152B LEU* 5.6 2.5 - - + -
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Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B THR* 4.6 4.7 + - - +
60B ILE* 3.6 6.1 - - - +
61B SER* 2.7 61.9 + - - +
74B TYR* 1.3 80.9 - - - +
76B THR* 1.3 62.0 + - - +
77B ARG* 3.0 33.4 + - - +
79B VAL 3.3 15.5 - - - +
80B SER* 4.1 1.8 - - - -
95B PHE* 3.6 37.5 - - + +
98B THR* 4.6 7.2 - - - +
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B THR 4.9 1.6 - - - -
60B ILE* 4.5 3.1 - - - -
74B TYR* 4.0 4.8 - - + -
75B ARG* 1.3 73.2 - - - +
77B ARG* 1.3 66.0 + - - +
78B ASP 2.5 18.7 + - - -
79B VAL* 3.0 15.9 + - + +
81B TYR* 3.8 28.7 - - + +
137B LEU 3.8 15.7 - - - +
138B PHE* 2.6 44.4 + - - +
140B TYR* 4.9 3.6 - - + -
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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