Contacts of the strand formed by residues 62 - 70 (chain A) in PDB entry 2DLZ
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 VAL 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ASP* 3.2 39.7 + - - +
32A LEU* 3.5 36.8 - - + -
33A LYS* 3.7 10.3 - - - +
55A SER* 3.3 13.5 - - - +
56A ILE 4.2 4.9 - - - +
57A LYS* 3.7 11.6 - - + +
61A GLU* 1.3 69.1 - - - +
63A LYS* 1.3 61.6 + - - +
64A HIS* 3.3 32.3 - - - +
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Residues in contact with LYS 63 (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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54A ILE 3.8 1.3 - - - +
55A SER* 2.9 27.0 + - - -
56A ILE* 3.3 14.9 + - + +
58A PHE* 3.5 12.3 - - - +
59A ASN* 4.7 6.2 - - - +
61A GLU* 2.9 60.2 + - - +
62A VAL* 1.3 76.2 + - - +
64A HIS* 1.3 60.8 + - - +
65A ILE* 4.1 6.5 - - + -
104A LEU* 3.4 37.0 - - + -
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Residues in contact with HIS 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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25A ARG* 4.7 18.3 - - + +
28A THR* 3.7 23.6 - - + +
29A ASP* 4.9 7.5 + - - +
43A ARG* 3.8 23.1 + - - -
45A ARG* 6.0 0.4 + - - -
53A ALA* 6.1 1.8 - - + +
54A ILE 3.7 2.9 - - - -
55A SER* 3.1 23.6 + - - -
62A VAL* 3.3 24.4 + - + +
63A LYS* 1.3 74.2 - - - +
65A ILE* 1.3 65.5 + - - +
66A LYS 4.2 0.2 + - - -
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Residues in contact with ILE 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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53A ALA* 3.1 10.6 - - - +
54A ILE* 2.8 44.5 + - + +
56A ILE* 4.0 24.7 - - + -
63A LYS* 5.3 5.4 - - + -
64A HIS* 1.3 78.8 - - - +
66A LYS* 1.3 74.6 + - + +
76A ILE* 3.9 26.7 - - + -
97A LEU* 4.3 16.6 - - + -
101A PHE* 3.7 37.5 - - + -
104A LEU* 4.8 4.9 - - + -
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Residues in contact with LYS 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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45A ARG* 6.1 2.9 - - + -
50A GLU* 3.6 23.8 + - + -
52A PHE 4.1 3.4 - - - +
53A ALA* 4.5 1.3 - - - +
64A HIS 4.2 0.4 + - - -
65A ILE* 1.3 80.1 - - + +
67A VAL* 1.3 60.4 + - - +
68A VAL* 3.5 31.0 - - + +
76A ILE* 3.2 19.2 - - - +
77A THR* 4.6 10.1 + - - +
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Residues in contact with VAL 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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50A GLU* 3.0 29.1 - - - +
51A ARG 4.1 0.9 + - - +
52A PHE* 2.8 51.8 + - + +
53A ALA* 3.7 8.1 - - - +
54A ILE* 4.2 16.4 - - + -
66A LYS* 1.3 75.3 - - - +
68A VAL* 1.3 69.1 + - - +
69A GLU* 4.9 1.1 - - + +
74A ILE* 3.8 29.4 - - + -
75A HIS 3.8 7.0 - - - +
76A ILE* 3.9 13.0 - - + -
85A LEU* 4.4 7.2 - - + -
88A LEU* 5.3 0.7 - - + -
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Residues in contact with VAL 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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49A ALA* 5.5 2.0 - - + +
50A GLU* 3.6 17.9 - - - +
66A LYS* 3.5 34.1 + - + +
67A VAL* 1.3 73.7 - - - +
69A GLU* 1.3 67.2 + - - +
70A LYS* 4.0 10.2 + - + +
73A TRP 3.7 0.7 - - - +
74A ILE* 3.6 2.8 - - - -
75A HIS* 2.8 60.1 + - + +
77A THR* 5.0 7.4 - - - +
78A GLU 5.7 1.1 - - - +
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Residues in contact with GLU 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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48A GLU 5.6 0.4 - - - +
49A ALA* 3.5 30.1 + - - +
51A ARG* 5.6 3.6 - - + +
52A PHE* 5.8 6.7 - - + -
67A VAL* 4.1 2.4 + - + -
68A VAL* 1.3 74.0 - - - +
70A LYS* 1.3 72.8 + - - +
71A ASP 4.3 0.2 + - - -
72A ASN* 3.8 16.9 + - - -
73A TRP 3.2 17.8 - - - +
74A ILE* 3.7 22.0 - - + -
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Residues in contact with LYS 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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68A VAL* 4.0 15.4 + - + -
69A GLU* 1.3 77.1 + - - +
71A ASP* 1.3 88.3 + - - +
72A ASN 3.1 2.2 - - - -
73A TRP* 2.8 28.5 + - - +
75A HIS* 4.7 10.9 + - - +
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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