Contacts of the strand formed by residues 71 - 77 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C LYS* 4.9 2.7 - - - +
38C TYR* 3.2 28.7 - - + -
40C VAL* 3.5 34.5 - - - -
63C ALA 4.9 0.2 - - - +
66C PHE* 3.0 46.4 + - + +
67C LYS* 3.5 7.3 + - - +
69C LEU* 4.0 6.7 - - + +
70C ASN* 1.3 78.1 - - - +
72C GLN* 1.3 63.0 + - - +
73C VAL 3.9 0.3 + - - -
160C VAL* 4.2 12.1 - - + -
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Residues in contact with GLN 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C TYR* 3.5 37.7 - - + -
37C LYS* 3.6 25.3 - - - +
38C TYR 2.8 14.1 + - - +
39C VAL* 3.2 9.2 - - + +
40C VAL 3.0 21.5 + - - -
70C ASN 4.3 0.2 - - - -
71C CYS* 1.3 72.5 - - - +
73C VAL* 1.3 86.8 + - - +
74C ILE* 3.8 10.5 - - + -
101C ASN 5.1 1.4 - - - +
102C ILE* 4.7 5.9 - - - +
103C PRO* 3.6 15.2 - - - +
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Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 3.4 17.0 - - + +
42C PHE* 4.2 21.3 - - + -
59C PHE* 4.6 9.4 - - + +
63C ALA* 5.2 4.0 - - + -
66C PHE* 3.4 49.4 - - + -
71C CYS 3.9 0.8 + - - -
72C GLN* 1.3 92.6 + - - +
74C ILE* 1.3 66.1 + - - +
102C ILE* 3.6 35.8 - - + +
103C PRO* 3.6 9.2 - - - +
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Residues in contact with ILE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PHE* 5.0 6.5 - - + -
29C ILE* 5.1 2.2 - - + -
31C LEU* 4.7 7.6 - - + -
34C TYR* 3.9 33.0 - - + -
39C VAL* 3.8 21.5 - - + -
40C VAL 2.8 12.1 + - - +
41C PHE* 3.4 20.0 - - + -
42C PHE* 2.9 27.5 + - - +
72C GLN* 3.8 12.6 - - + -
73C VAL* 1.3 86.5 - - - +
75C GLY* 1.3 64.0 + - - +
103C PRO* 4.0 16.8 - - + +
105C VAL* 3.9 28.0 - - + -
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Residues in contact with GLY 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C PHE* 3.6 13.5 - - - -
44C TYR* 5.4 3.6 - - - -
48C PHE* 5.7 1.6 - - - -
56C ILE* 6.0 2.2 - - - -
74C ILE* 1.3 75.7 - - - +
76C ALA* 1.3 54.3 + - - +
102C ILE* 4.3 8.5 - - - +
103C PRO 3.2 10.4 + - - +
104C LEU* 3.1 20.3 - - - -
105C VAL 2.7 29.8 + - - -
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C PHE* 3.7 22.2 - - + -
42C PHE* 2.8 15.4 + - - +
43C PHE* 3.7 16.8 - - + -
44C TYR* 2.8 31.6 + - - -
48C PHE* 5.0 1.3 - - - -
75C GLY* 1.3 76.3 - - - +
77C SER* 1.3 65.1 + - - +
84C HIS* 4.9 1.6 - - - -
105C VAL* 3.2 20.9 - - + +
107C ASP* 6.0 0.2 - - + -
112C ILE* 5.7 0.2 - - + -
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Residues in contact with SER 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C PHE* 4.4 3.4 - - - -
44C TYR* 3.2 18.2 - - - -
46C LEU 4.3 2.5 - - - -
48C PHE* 3.6 20.1 - - - -
76C ALA* 1.3 78.8 - - - +
78C VAL* 1.3 60.1 + - - +
79C ASP* 2.6 30.4 + - - +
84C HIS* 2.9 16.7 + - - -
105C VAL 3.1 8.3 + - - +
106C SER* 3.7 0.2 - - - -
107C ASP* 3.0 27.5 + - - +
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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