Contacts of the strand formed by residues 63 - 70 (chain A) in PDB entry 3CY2
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 PRO 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLY 3.7 1.8 - - - +
56A ILE* 4.7 2.0 - - + -
61A ASN 3.3 7.4 - - - +
62A LEU* 1.3 97.0 - - + +
64A VAL* 1.3 63.1 + - - +
121A GLU* 4.1 2.3 - - - +
122A ARG* 3.2 63.1 + - - +
124A GLU* 4.4 15.9 - - + -
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.8 26.0 - - + -
55A GLY* 2.9 44.9 + - - -
56A ILE 3.8 2.9 - - - +
57A ARG* 4.2 3.1 - - + +
62A LEU* 3.4 13.9 + - + +
63A PRO* 1.3 79.7 - - - +
65A ALA* 1.3 57.9 + - - +
66A ILE* 4.2 8.1 - - + -
107A LEU* 3.7 26.5 - - + -
119A ILE* 3.8 15.5 - - + -
120A LEU 3.2 8.7 - - - +
122A ARG* 2.7 29.8 + - - -
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 4.6 2.9 - - + -
52A VAL* 3.9 12.8 - - + -
53A TYR 3.3 6.7 - - - +
64A VAL* 1.3 74.3 - - - +
66A ILE* 1.3 61.5 + - - +
67A LYS 3.9 0.8 + - - -
118A LEU 3.4 4.0 - - - +
119A ILE* 3.5 2.9 - - - +
120A LEU* 2.8 42.0 + - + +
122A ARG* 3.8 1.9 - - + +
501A MB9 3.7 42.4 - - + -
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.9 7.0 - - + -
38A TYR* 4.0 24.7 - - + -
40A VAL* 4.2 26.9 - - + -
52A VAL* 3.3 3.2 - - - -
53A TYR* 2.8 41.6 + - + +
54A SER 4.5 2.0 - - - +
55A GLY* 4.1 17.5 - - - -
64A VAL* 4.2 9.6 - - + -
65A ALA* 1.3 74.1 - - - +
67A LYS* 1.3 58.2 + - - +
68A HIS* 3.6 19.9 - - + +
117A VAL* 3.4 30.1 - - + -
118A LEU 3.5 2.5 - - - -
119A ILE* 4.1 15.7 - - + -
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 3.8 20.1 - - + +
51A SER 3.6 5.8 - - - +
52A VAL* 4.2 6.1 - - + -
66A ILE* 1.3 72.8 - - - +
68A HIS* 1.3 63.7 + - - +
69A VAL* 3.8 21.1 + - + +
89A GLU* 2.6 32.3 + - - +
116A PHE 3.5 1.7 - - - +
117A VAL* 3.3 3.6 - - - -
118A LEU* 2.7 51.1 + - + +
120A LEU* 4.3 12.1 - - + -
186A ASP* 4.1 13.9 + - - -
188A GLY* 5.2 0.4 - - - -
401A CL 3.2 23.4 - - + +
501A MB9 3.1 32.3 + - - +
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Residues in contact with HIS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 5.2 2.2 - - + -
49A PHE 4.5 0.2 - - - -
50A GLY* 3.2 8.0 - - - -
51A SER* 2.8 38.4 + - - +
53A TYR* 3.6 36.0 - + - -
66A ILE* 3.6 22.4 - - + +
67A LYS* 1.3 73.2 - - - +
69A VAL* 1.3 62.6 + - - +
70A GLU 4.0 0.8 + - - -
112A ARG* 3.4 31.7 + - - -
115A SER* 5.1 7.3 + - - -
116A PHE 3.5 4.7 - - - +
117A VAL* 3.8 19.5 - - + +
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 3.7 13.5 - - + +
67A LYS* 4.0 28.0 - - + +
68A HIS* 1.3 76.3 - - - +
70A GLU* 1.3 63.2 + - - +
71A LYS 3.6 0.3 + - - -
73A ARG 5.9 0.9 - - - -
74A ILE* 3.6 32.0 - - + +
87A PRO* 5.0 5.6 - - + -
89A GLU* 4.0 23.6 - - - +
115A SER* 3.2 3.5 - - - -
116A PHE* 2.9 44.0 + - + +
118A LEU* 4.7 8.7 - - + -
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE 3.8 9.5 + - - +
50A GLY* 4.9 5.6 - - - -
68A HIS 4.0 2.2 + - - +
69A VAL* 1.3 75.0 - - - +
71A LYS* 1.3 63.7 + - - +
72A ASP* 3.2 12.3 - - + +
73A ARG* 3.3 22.8 + - + +
74A ILE* 3.4 12.2 + - - +
114A ASP* 3.7 12.1 - - + +
115A SER* 4.2 4.9 - - - -
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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