Contacts of the strand formed by residues 71 - 77 (chain D) in PDB entry 4XCS
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 CYS 71 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LYS* 4.9 2.9 - - - +
38D TYR* 3.3 28.0 - - + -
39D VAL 4.1 0.4 - - - -
40D VAL* 3.5 31.6 - - - -
63D ALA 4.9 0.2 - - - +
66D PHE* 2.8 53.4 + - + +
67D LYS* 3.6 6.3 + - - +
69D LEU* 4.2 9.9 - - + +
70D ASN* 1.3 74.7 - - - +
72D GLN* 1.3 63.7 + - - +
73D VAL 3.9 0.2 + - - -
160D VAL* 4.2 9.0 - - + -
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Residues in contact with GLN 72 (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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34D TYR* 3.4 44.5 - - + -
37D LYS* 3.4 22.5 - - - +
38D TYR 2.8 12.6 + - - +
39D VAL* 3.2 8.3 - - + +
40D VAL 2.9 24.1 + - - -
70D ASN 4.3 0.4 - - - -
71D CYS* 1.3 72.2 - - - +
73D VAL* 1.3 80.6 + - - +
74D ILE* 3.8 14.6 - - + -
101D ASN 5.3 1.0 - - - +
102D ILE* 5.0 2.1 - - - +
103D PRO* 3.4 17.3 - - - +
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Residues in contact with VAL 73 (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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40D VAL* 3.4 14.8 - - + +
42D PHE* 3.9 24.5 - - + -
59D PHE* 4.0 15.7 - - + +
63D ALA* 5.4 2.5 - - + -
66D PHE* 3.5 48.0 - - + -
71D CYS 3.9 0.4 + - - -
72D GLN* 1.3 94.7 + - - +
74D ILE* 1.3 63.1 + - - +
102D ILE* 3.7 28.5 - - + +
103D PRO* 3.5 9.9 - - - +
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Residues in contact with ILE 74 (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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15D PHE* 5.7 2.0 - - + -
29D ILE* 4.8 4.7 - - + -
31D LEU* 5.0 10.5 - - + -
34D TYR* 3.8 33.0 - - + +
39D VAL* 4.2 14.1 - - + -
40D VAL 2.9 10.0 + - - +
41D PHE* 3.3 15.7 - - + -
42D PHE* 3.0 29.2 + - - -
72D GLN* 3.8 13.5 - - + -
73D VAL* 1.3 80.6 - - - +
75D GLY* 1.3 71.5 + - - +
102D ILE* 5.1 0.2 - - - -
103D PRO* 3.7 21.3 - - + +
105D VAL* 3.7 22.2 - - + -
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Residues in contact with GLY 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D PHE* 3.3 29.5 - - - -
44D TYR* 4.7 0.2 - - - -
74D ILE* 1.3 77.9 - - - +
76D ALA* 1.3 61.8 + - - +
102D ILE* 4.4 2.2 - - - +
103D PRO 3.1 9.5 + - - -
104D LEU* 3.4 17.1 - - - +
105D VAL 2.8 24.4 + - - -
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Residues in contact with ALA 76 (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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41D PHE* 3.6 29.4 - - + -
42D PHE 2.8 11.3 + - - +
43D PHE* 3.2 18.5 - - + -
44D TYR* 3.0 34.9 + - - -
75D GLY* 1.3 76.5 - - - +
77D SER* 1.3 63.8 + - - +
84D HIS* 4.9 0.7 - - - -
105D VAL* 3.4 18.6 - - + +
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Residues in contact with SER 77 (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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43D PHE* 3.9 11.7 - - - -
44D TYR* 3.2 34.8 - - - -
45D PRO 4.0 3.4 - - - -
76D ALA* 1.3 74.5 - - - +
78D VAL* 1.3 60.6 + - - +
79D ASP* 2.6 32.1 + - - +
84D HIS* 3.1 13.6 + - - -
105D VAL 3.3 7.6 + - - +
107D ASP* 3.0 24.1 + - - +
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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