Contacts of the strand formed by residues 94 - 101 (chain B) in PDB entry 2YD7
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 ALA 94 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LYS* 3.7 29.6 - - + -
60B LYS* 3.7 17.5 - - - +
92B ASP 3.0 7.5 + - - +
93B GLU* 1.3 77.5 - - - +
95B ILE* 1.3 68.3 + - - +
96B TYR* 3.5 11.0 - - + -
112B ARG* 3.8 3.0 - - - +
113B LEU 3.1 26.7 + - - -
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Residues in contact with ILE 95 (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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102A ASN 4.8 2.0 - - - +
103A ASN* 3.3 32.8 - - - +
104A VAL 4.1 7.0 - - - +
105A GLY* 4.3 7.9 - - - +
106A GLU* 5.6 0.2 - - + -
59B LYS* 4.0 1.0 - - - -
60B LYS* 3.5 29.2 + - + +
94B ALA* 1.3 78.8 - - - +
96B TYR* 1.3 65.8 + - - +
97B GLU* 4.1 12.7 - - - +
110B SER* 3.7 29.8 - - - +
111B THR 3.5 7.2 - - - +
112B ARG* 4.2 23.3 - - + +
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Residues in contact with TYR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 4.5 7.9 - + + -
57B TRP* 4.9 3.6 - - + -
58B ASN 3.3 13.9 - - - +
59B LYS* 3.7 31.9 + - + -
64B VAL* 4.4 3.1 - - + -
69B PHE* 3.5 38.4 - + - -
82B LEU* 4.2 23.1 - - + -
84B ILE* 4.5 3.1 - - + -
92B ASP* 2.7 35.6 + - - +
94B ALA* 3.5 19.3 - - + -
95B ILE* 1.3 73.0 - - - +
97B GLU* 1.3 62.7 + - - +
98B CYS 4.3 0.2 + - - -
110B SER* 3.1 3.8 - - - -
111B THR* 2.8 47.4 + - + +
113B LEU* 3.8 18.6 - - + -
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Residues in contact with GLU 97 (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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106A GLU* 3.8 37.9 - - + +
56B VAL 3.7 0.3 - - - +
57B TRP* 3.2 15.4 - - - -
58B ASN* 2.8 52.9 + - + +
60B LYS* 3.6 9.6 + - - -
61B GLY* 3.1 30.3 + - - -
95B ILE* 4.1 11.2 - - - +
96B TYR* 1.3 77.5 - - - +
98B CYS* 1.3 59.7 + - - +
99B VAL* 4.6 10.3 - - + +
108B SER* 5.2 4.5 - - - +
109B VAL 3.4 6.1 - - - +
110B SER* 4.1 12.8 - - - -
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Residues in contact with CYS 98 (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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26B PHE* 3.8 8.7 - - - -
30B PRO* 4.4 3.7 - - + +
45B CYS* 2.0 54.1 - - + -
55B ILE* 3.5 21.1 - - - -
56B VAL 3.7 2.5 - - - -
57B TRP* 4.0 13.8 - - + -
96B TYR 4.3 0.2 + - - -
97B GLU* 1.3 72.1 - - - +
99B VAL* 1.3 61.6 + - - +
108B SER* 3.1 5.0 - - - -
109B VAL* 2.8 42.5 + - + +
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Residues in contact with VAL 99 (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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108A SER* 5.7 0.4 - - - +
54B LYS 3.7 1.0 - - - +
55B ILE* 3.4 4.0 - - - -
56B VAL* 2.8 49.8 + - + +
58B ASN* 3.6 27.6 - - - +
97B GLU* 4.6 7.4 - - + -
98B CYS* 1.3 78.0 - - - +
100B ALA* 1.3 62.8 - - - +
101B SER* 5.0 2.4 + - - +
106B GLU* 3.7 33.0 - - - +
107B ILE 3.4 9.4 - - - +
108B SER* 3.7 15.9 - - - -
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Residues in contact with ALA 100 (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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24B PRO* 3.7 8.4 - - + +
26B PHE* 3.8 13.4 - - + -
47B ALA* 3.7 21.5 - - + -
53B PRO* 4.4 1.3 - - + -
54B LYS 3.3 4.9 - - - +
55B ILE* 3.5 21.8 - - + -
98B CYS 4.1 0.8 - - - -
99B VAL* 1.3 71.4 - - - +
101B SER* 1.3 62.4 + - - +
106B GLU* 3.3 2.8 - - - +
107B ILE* 2.8 43.2 + - + -
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Residues in contact with SER 101 (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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24B PRO* 3.8 5.1 - - - +
52B ARG 4.7 0.2 - - - +
53B PRO* 3.1 3.5 - - - +
54B LYS* 2.9 51.9 + - - +
56B VAL* 5.5 1.9 - - - +
99B VAL* 5.0 3.1 + - - +
100B ALA* 1.3 74.4 - - - +
102B ASN* 1.3 62.5 + - - +
105B GLY 3.4 4.5 - - - -
106B GLU* 3.3 35.6 + - - -
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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