Contacts of the strand formed by residues 58 - 65 (chain D) in PDB entry 1REW
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 HIS 58 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D LEU* 3.8 7.4 - - - -
38D CYS* 4.1 1.3 - - - -
55D THR* 3.8 2.6 - - - +
57D GLY* 1.3 79.3 - - - +
59D CYS* 1.3 65.7 + - - +
77D CYS* 3.6 3.1 - - - -
78D MET* 2.8 38.7 + - + +
80D TYR* 3.7 14.3 - + - -
83D SER* 3.1 39.6 + - - -
87D CYS* 4.3 10.7 - - - -
101D CYS* 4.0 18.6 - - + +
102D CYS 3.6 11.7 + - - +
103D ARG* 3.5 26.4 - - - +
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Residues in contact with CYS 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LEU* 3.8 10.3 - - - +
37D LYS 3.7 7.9 - - - -
38D CYS* 2.0 52.5 - - - -
58D HIS* 1.3 74.7 - - - +
60D PHE* 1.3 59.7 + - - +
76D GLY 3.4 2.2 - - - -
101D CYS* 3.2 4.9 - - - +
102D CYS* 2.8 31.0 + - - -
104D THR 4.0 1.6 - - - -
106D LEU 4.1 0.7 - - - -
107D CYS* 3.5 31.2 - - - -
108D ASN* 3.6 16.2 - - - -
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Residues in contact with PHE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PRO* 3.6 28.5 - - + -
52B ALA* 4.5 5.6 - - + -
43D HIS* 3.7 33.4 - + + -
59D CYS* 1.3 75.0 - - - +
61D ALA* 1.3 70.6 + - - +
62D ILE* 4.0 6.7 - - + -
75D SER* 3.3 4.8 - - - -
76D GLY* 2.9 60.3 + - - -
77D CYS 3.5 21.5 - - - -
78D MET* 4.1 13.5 - - + -
99D ILE* 4.1 18.8 - - + -
100D GLU 3.2 12.1 - - - +
101D CYS* 4.1 8.3 - - - -
102D CYS* 5.6 0.2 - - - -
108D ASN* 2.9 24.2 + - - -
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Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D PHE* 1.3 75.3 - - - +
62D ILE* 1.3 61.4 + - - +
73D LEU* 4.6 2.5 - - + -
74D ALA 3.4 9.9 - - - +
75D SER* 4.1 5.8 - - - +
99D ILE* 3.5 2.1 - - - +
100D GLU 2.9 30.7 + - - -
108D ASN* 4.4 3.5 - - + +
111D LEU* 3.6 44.6 - - + +
113D PRO* 3.9 11.0 - - + +
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Residues in contact with ILE 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PHE* 3.8 37.5 - - + +
50B PRO* 4.0 11.4 - - + -
43D HIS* 4.4 1.3 - - - +
60D PHE* 4.0 16.6 - - + -
61D ALA* 1.3 76.3 - - - +
63D ILE* 1.3 71.2 + - - +
64D GLU* 4.0 23.2 - - - +
72D THR 3.8 1.0 - - - +
73D LEU* 3.4 7.6 - - - +
74D ALA* 2.8 50.6 + - + +
97D ARG* 4.2 12.8 - - + -
98D THR 3.3 16.2 - - - +
99D ILE* 4.1 10.8 - - + -
113D PRO* 4.6 0.2 - - - -
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ILE* 1.3 72.7 - - - +
64D GLU* 1.3 63.6 + - - +
71D THR* 4.8 10.5 - - - +
72D THR 3.4 11.9 - - - +
73D LEU* 4.3 12.5 - - + +
97D ARG* 3.1 5.0 - - - +
98D THR* 2.9 46.7 + - - +
112D GLN* 5.4 6.7 - - + -
113D PRO* 3.6 44.7 - - + +
114D THR 4.3 0.4 - - - -
115D LEU* 3.9 32.3 - - + +
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Residues in contact with GLU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PHE 4.4 9.7 - - - +
43D HIS* 4.9 5.0 + - - -
62D ILE* 4.0 29.1 - - + +
63D ILE* 1.3 77.1 - - - +
65D GLU* 1.3 62.6 + - - +
66D ASP* 4.1 1.3 + - + +
70D GLU 3.7 1.2 - - - +
71D THR* 3.2 4.4 - - - -
72D THR* 2.9 53.0 + - - +
74D ALA* 5.0 4.9 - - - +
95D LEU* 6.2 0.8 - - + +
96D ARG 3.6 5.4 - - - +
97D ARG* 3.8 17.5 - - + -
115D LEU* 4.3 2.2 - - - -
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Residues in contact with GLU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D GLU* 1.3 74.7 - - - +
66D ASP* 1.3 67.1 + - - +
69D GLY* 3.8 34.7 - - - +
70D GLU 3.4 4.3 - - - -
71D THR* 3.8 15.2 - - + +
95D LEU* 3.5 24.8 - - - +
96D ARG* 2.9 66.1 + - + +
115D LEU* 4.3 4.2 - - + +
118D VAL* 5.5 0.2 - - - +
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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