Contacts of the strand formed by residues 64 - 74 (chain A) in PDB entry 4ES7
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 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A TRP* 3.4 11.3 - - - -
61A ARG 2.9 35.6 + - - +
62A LYS* 6.0 0.4 - - + -
63A GLY* 1.3 86.7 - - - +
65A CYS* 1.3 65.1 + - - +
66A GLU* 3.4 29.4 + - + +
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Residues in contact with CYS 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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58A THR* 3.7 10.1 - - - -
59A ARG 3.7 0.2 - - - -
60A TRP* 3.8 7.7 - - + -
64A VAL* 1.3 78.1 - - - +
66A GLU* 1.3 59.2 + - - +
67A GLU 3.9 2.1 + - - -
162A CYS* 2.1 65.5 - - + -
163A VAL 3.8 7.6 - - - +
164A PRO* 3.9 23.4 - - + +
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Residues in contact with GLU 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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57A SER 3.6 1.9 - - - +
58A THR* 3.3 4.3 - - - -
59A ARG* 2.8 42.7 + - + +
61A ARG* 3.7 41.7 + - + +
64A VAL* 3.9 23.1 - - + +
65A CYS* 1.3 72.6 - - - +
67A GLU* 1.3 64.0 + - - +
68A THR* 4.1 4.0 + - - +
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Residues in contact with GLU 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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56A THR* 3.6 32.0 - - + +
57A SER 3.3 6.3 - - - +
58A THR* 4.1 10.0 + - - +
65A CYS 3.9 2.4 + - - -
66A GLU* 1.3 78.8 + - - +
68A THR* 1.3 64.7 + - - +
69A SER* 4.3 10.3 + - - -
164A PRO* 3.9 25.6 - - + +
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Residues in contact with THR 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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55A MET 4.0 0.3 - - - +
56A THR* 3.5 3.6 - - - +
57A SER* 2.8 44.2 + - - -
59A ARG* 5.5 4.3 + - - -
66A GLU* 5.0 4.3 + - - +
67A GLU* 1.3 76.0 + - - +
69A SER* 1.3 70.5 + - - +
83A TYR* 5.4 5.8 - - - +
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Residues in contact with SER 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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54A SER* 5.0 3.3 + - - -
55A MET 3.3 9.7 + - - -
56A THR* 4.0 10.8 + - - +
67A GLU* 4.2 13.9 + - - -
68A THR* 1.3 83.5 - - - +
70A GLY* 1.3 62.1 + - - +
83A TYR* 4.5 5.4 + - - -
85A LYS* 5.6 1.7 + - - -
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Residues in contact with GLY 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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54A SER* 3.8 4.0 + - - -
55A MET* 2.9 38.9 + - - +
69A SER* 1.3 77.6 + - - +
71A ALA* 1.3 60.9 + - - -
72A TYR* 4.1 2.7 - - - -
83A TYR* 4.2 20.2 - - - -
85A LYS* 6.0 0.4 - - - -
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Residues in contact with ALA 71 (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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47A GLY* 6.2 0.7 - - - -
52A GLU* 3.3 28.7 - - + +
53A ILE 3.6 6.1 - - - +
54A SER* 4.9 1.6 - - - +
70A GLY* 1.3 71.9 - - - -
72A TYR* 1.3 63.1 + - - +
73A GLU* 4.2 4.6 + - - +
82A LEU 4.4 1.4 - - - +
83A TYR* 3.7 17.2 - - - -
84A HIS 5.4 0.5 + - - -
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Residues in contact with TYR 72 (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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52A GLU* 3.3 6.8 - - - +
53A ILE* 2.9 43.6 + - + +
55A MET* 3.3 45.6 - - + +
70A GLY* 4.9 2.2 - - - -
71A ALA* 1.3 80.7 - - - +
73A GLU* 1.3 62.8 + - - +
81A PHE* 3.9 29.6 - + + -
82A LEU 3.3 5.6 - - - +
83A TYR* 3.4 54.1 - + + -
92A MET* 5.3 3.9 - - + +
94A SER* 3.9 23.9 + - - -
109A THR* 5.7 1.7 - - - +
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Residues in contact with GLU 73 (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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51A ALA 3.8 5.6 - - - +
52A GLU* 4.6 13.9 - - + +
53A ILE* 5.8 0.4 - - - -
71A ALA* 4.8 4.3 - - + +
72A TYR* 1.3 77.5 - - - +
74A LYS* 1.3 69.0 + - - +
75A THR* 3.9 0.6 - - + +
81A PHE* 3.3 6.5 - - - -
82A LEU* 2.6 54.7 + - + +
84A HIS* 4.7 16.8 + - - +
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Residues in contact with LYS 74 (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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11A ILE* 3.7 32.2 - - + +
15A TYR* 4.4 10.3 + - - -
50A GLU 2.7 28.7 + - - -
51A ALA* 3.0 31.7 + - + +
52A GLU* 4.4 3.0 + - - +
53A ILE* 4.4 10.9 - - + +
72A TYR 4.0 1.0 + - - -
73A GLU* 1.3 81.7 - - - +
75A THR* 1.3 65.7 + - - +
77A THR 6.0 0.4 - - - +
78A ASP* 5.5 6.7 - - - +
80A LYS 4.4 3.6 - - - +
81A PHE* 4.4 12.8 - - + -
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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