Contacts of the strand formed by residues 38 - 43 (chain E) 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 TYR 38 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E LYS* 1.3 75.6 - - - +
39E VAL* 1.3 55.4 + - - +
70E ASN* 3.2 6.6 + - - +
71E CYS* 3.1 18.5 - - + -
72E GLN 2.8 30.7 + - - -
132E ILE* 4.0 21.1 - - + -
133E ILE 3.4 14.6 - - - -
134E ASP* 3.4 22.4 - - + +
135E ASP* 3.5 26.4 - - + +
140E ARG* 3.5 6.4 + - + -
160E VAL* 4.3 10.5 - - + -
163E PHE* 3.4 31.6 - + + +
164E GLN* 3.5 37.0 - - + +
167E ASP* 2.6 31.6 + - - -
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Residues in contact with VAL 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LEU* 4.7 9.9 - - + +
34E TYR* 3.8 30.5 - - + +
37E LYS 3.9 6.5 - - - +
38E TYR* 1.3 81.2 - - - +
40E VAL* 1.3 74.8 + - - +
41E PHE* 4.0 10.8 - - + +
71E CYS* 4.2 0.7 - - - -
72E GLN* 3.2 11.9 - - + +
74E ILE* 4.1 19.7 - - + -
131E PHE 3.5 3.8 - - - +
132E ILE* 3.6 3.8 - - - +
133E ILE* 2.9 54.2 + - + +
134E ASP 5.5 0.2 - - - +
160E VAL* 6.2 0.2 - - - -
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Residues in contact with VAL 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E VAL* 1.3 72.6 - - - +
41E PHE* 1.3 54.9 + - - +
42E PHE* 4.6 8.5 - - + -
59E PHE* 4.4 12.8 - - + -
66E PHE* 3.9 12.8 - - + -
71E CYS* 3.5 22.6 - - - -
72E GLN 2.9 7.3 + - - +
73E VAL* 3.3 10.4 - - + +
74E ILE 2.8 32.2 + - - +
130E LEU* 3.8 25.8 - - + -
131E PHE 3.6 4.0 - - - -
132E ILE* 4.1 7.0 - - + -
156E THR* 4.0 11.4 - - + -
160E VAL* 3.8 20.0 - - + -
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Residues in contact with PHE 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E PHE* 3.6 30.5 - + - -
31E LEU* 4.7 6.3 - - + -
39E VAL* 3.8 5.8 - - + -
40E VAL* 1.3 72.0 - - - +
42E PHE* 1.3 58.1 + - - +
43E PHE* 3.7 33.2 - + - -
74E ILE* 3.3 27.8 - - + -
76E ALA* 3.7 21.3 - - + -
105E VAL* 4.5 2.7 - - + -
112E ILE* 4.4 3.1 - - + -
116E TYR* 3.7 40.2 - + - -
130E LEU* 4.3 0.2 - - - +
131E PHE* 2.7 50.6 + + + +
133E ILE* 4.1 14.4 - - + -
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Residues in contact with PHE 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E VAL* 4.5 7.9 - - + -
41E PHE* 1.3 75.7 - - - +
43E PHE* 1.3 59.6 + - - +
44E TYR* 3.9 25.4 - + + -
55E GLU* 5.0 13.9 - - + -
56E ILE* 4.0 26.7 - - + -
59E PHE* 4.3 22.2 - + + -
73E VAL* 3.8 26.5 - - + -
74E ILE 3.0 14.4 + - - -
75E GLY* 3.3 18.1 - - - -
76E ALA* 2.7 33.3 + - - +
102E ILE* 4.1 13.7 - - + -
129E GLY 3.3 9.9 - - - +
130E LEU* 4.3 13.5 - - + -
151E ARG* 5.2 7.9 - - - +
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Residues in contact with PHE 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E PHE* 3.7 33.9 - + - -
42E PHE* 1.3 76.9 - - - +
44E TYR* 1.3 60.3 + - - +
55E GLU* 5.3 1.7 - - - +
76E ALA* 3.1 17.9 - - + -
77E SER* 3.9 25.4 - - - -
78E VAL 4.4 0.4 - - - -
105E VAL* 6.0 0.2 - - + -
107E ASP* 4.2 7.0 - - + -
112E ILE* 3.8 16.6 - - + -
113E ALA* 3.8 35.7 - - + -
116E TYR* 4.3 5.2 - - + -
118E VAL* 3.9 15.0 - - + -
126E SER* 3.4 24.9 - - - +
127E PHE 4.2 1.3 - - - +
128E ARG* 3.4 5.4 - - - +
129E GLY* 2.9 38.6 + - - +
131E PHE* 4.4 9.4 - + + -
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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