Contacts of the strand formed by residues 38 - 44 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37F LYS* 1.3 77.7 - - - +
39F VAL* 1.3 55.5 + - - +
70F ASN* 3.0 8.4 + - - +
71F CYS* 3.8 22.0 - - + -
72F GLN 2.8 28.4 + - - -
132F ILE* 4.0 20.6 - - + -
133F ILE 3.4 14.8 - - - -
134F ASP* 3.3 14.8 - - + +
135F ASP* 3.5 23.9 - - + +
140F ARG* 3.3 15.0 + - + -
160F VAL* 4.3 12.3 - - + -
163F PHE* 3.2 33.1 - + + +
164F GLN* 3.6 32.3 - - + +
167F ASP* 2.6 28.6 + - - -
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Residues in contact with VAL 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F LEU* 4.2 13.9 - - + -
34F TYR* 3.8 30.5 - - + -
37F LYS 4.0 5.8 - - - +
38F TYR* 1.3 81.6 - - - +
40F VAL* 1.3 74.6 + - - +
41F PHE* 4.1 12.3 - - + +
71F CYS* 4.3 0.2 - - - -
72F GLN* 3.3 13.5 - - + +
74F ILE* 3.7 20.6 - - + -
131F PHE 3.6 1.2 - - - +
132F ILE* 3.5 5.6 - - - +
133F ILE* 2.9 51.2 + - + +
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Residues in contact with VAL 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F VAL* 1.3 74.1 - - - +
41F PHE* 1.3 53.7 + - - +
42F PHE* 3.7 20.6 + - + -
59F PHE* 5.1 0.2 - - + -
66F PHE* 4.2 9.9 - - + -
71F CYS* 3.6 21.7 - - - -
72F GLN 3.1 5.7 + - - -
73F VAL* 3.4 15.2 - - + +
74F ILE 2.8 33.1 + - - +
130F LEU* 3.5 26.2 - - + -
131F PHE 3.6 3.6 - - - -
132F ILE* 4.9 6.5 - - + -
156F THR* 4.2 11.9 - - + -
160F VAL* 3.7 21.5 - - + -
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Residues in contact with PHE 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F PHE* 3.8 31.6 - + - -
31F LEU* 5.8 0.4 - - + -
39F VAL* 3.8 4.9 - - + -
40F VAL* 1.3 72.0 - - - +
42F PHE* 1.3 61.7 + - - +
43F PHE* 4.1 18.4 - + + -
74F ILE* 3.4 26.0 - - + -
76F ALA* 3.7 30.1 - - + -
105F VAL* 5.1 0.9 - - + -
112F ILE* 4.1 10.8 - - + -
116F TYR* 4.1 31.4 - + - -
130F LEU* 3.5 4.1 - - - -
131F PHE* 2.8 62.9 + + + +
133F ILE* 3.9 17.9 - - + -
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Residues in contact with PHE 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F VAL* 3.7 23.3 - - + -
41F PHE* 1.3 73.8 - - - +
43F PHE* 1.3 56.4 + - - +
44F TYR* 4.0 31.4 - + + -
55F GLU* 5.3 3.1 - - - -
56F ILE* 6.5 1.3 - - - -
59F PHE* 3.5 51.4 - + + -
73F VAL* 4.0 12.8 - - + -
74F ILE 3.0 16.3 + - - +
75F GLY* 3.6 5.5 - - - -
76F ALA* 2.8 35.4 + - - +
102F ILE* 5.8 2.0 - - + -
129F GLY 3.6 8.1 - - - +
130F LEU* 3.8 10.3 - - + -
151F ARG* 3.5 27.4 - - + -
201F GOL 4.4 7.2 - - - -
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Residues in contact with PHE 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F PHE* 3.9 8.4 + + + -
42F PHE* 1.3 72.9 - - - +
44F TYR* 1.3 79.8 + - - +
45F PRO* 3.4 14.2 - - + +
76F ALA* 3.8 23.1 - - + -
77F SER 4.4 2.5 - - - -
78F VAL* 4.2 6.7 - - + -
107F ASP* 3.3 33.7 - - + -
112F ILE* 3.6 29.8 - - + -
113F ALA* 3.5 20.9 - - + -
116F TYR* 5.6 0.9 - - + -
118F VAL* 3.6 20.0 - - + -
128F ARG* 3.6 2.8 - - - +
129F GLY 3.0 35.1 + - - +
131F PHE* 4.0 22.0 - - + -
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Residues in contact with TYR 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F PHE* 4.0 31.6 - + + -
43F PHE* 1.3 75.0 - - - +
45F PRO* 1.3 65.3 - - + +
46F LEU 3.2 18.0 + - - +
48F PHE* 3.6 13.2 - + - -
51F VAL* 3.5 29.2 - - + -
55F GLU* 2.6 34.1 + - - +
56F ILE* 3.4 34.7 + - + +
75F GLY* 5.4 2.2 - - - -
76F ALA 2.8 24.5 + - - +
77F SER* 3.2 24.4 - - - -
78F VAL 3.3 5.5 + - - -
128F ARG* 3.6 27.1 - - + -
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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