Contacts of the strand formed by residues 36 - 41 (chain A) in PDB entry 1XXE
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 GLY 36 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLY* 3.5 1.4 - - - -
35A THR* 1.3 83.6 - - - +
37A ILE* 1.3 63.9 + - - -
38A ARG* 3.8 0.8 + - - -
85A THR 2.7 24.9 + - - -
87A VAL 3.2 22.5 + - - +
239A GLY* 5.7 4.9 - - - -
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY* 1.3 76.9 - - - -
38A ARG* 1.3 62.7 + - - +
39A PHE* 5.0 2.2 - - + -
47A PRO* 3.9 1.6 - - - +
48A ALA* 3.0 34.9 + - + +
76A LEU* 4.3 10.3 - - + -
79A LEU* 3.9 23.8 - - + -
84A ILE* 3.3 26.5 - - + +
85A THR* 4.0 4.5 - - - +
87A VAL* 3.3 29.8 - - + -
89A ILE* 4.3 11.2 - - + -
236A TYR* 4.1 22.0 - - + +
239A GLY* 5.4 11.3 - - - +
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Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 4.3 6.0 + - - -
35A THR* 3.6 34.5 + - + +
36A GLY 4.5 3.6 - - - +
37A ILE* 1.3 76.7 - - - +
39A PHE* 1.3 68.0 + - - +
45A TYR* 4.0 29.4 - - + +
46A ILE 4.0 5.6 - - - +
47A PRO* 4.2 21.7 - - + +
48A ALA 4.3 0.4 - - - +
87A VAL 3.3 12.5 + - - +
88A THR* 3.5 22.9 - - + +
89A ILE* 2.9 25.5 + - - +
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Residues in contact with PHE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 5.0 1.8 - - + -
38A ARG* 1.3 76.3 - - - +
40A PHE* 1.3 62.2 + - - +
44A VAL 4.4 0.2 - - - -
45A TYR* 3.3 4.0 - - - +
46A ILE* 2.7 52.7 + - + +
48A ALA* 3.4 29.6 - - + -
62A LEU* 4.3 15.7 - - + -
69A ILE* 3.6 27.1 - - + -
72A VAL* 4.3 21.3 - - + -
75A ILE* 4.4 14.1 - - + -
76A LEU* 4.5 7.2 - - + -
88A THR* 5.2 0.4 - - - -
89A ILE* 3.2 46.7 - - + +
91A VAL* 3.6 15.5 - - + -
96A ILE* 5.0 2.5 - - + -
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Residues in contact with PHE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A PHE* 1.3 76.7 - - - +
41A LYS* 1.3 69.5 + - - +
42A ASN 4.4 1.1 - - - -
43A GLY* 3.4 36.8 - - - -
44A VAL 3.4 7.9 - - - -
45A TYR* 3.6 41.3 - + + -
46A ILE* 5.9 0.7 - - - -
88A THR* 4.3 13.5 - - + -
89A ILE 3.1 6.9 + - - -
90A GLU* 3.3 39.3 - - + +
91A VAL* 3.0 24.3 + - - +
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 1.3 84.7 - - - +
42A ASN* 1.3 109.9 + - - +
43A GLY 3.0 2.0 - - - -
44A VAL* 2.8 28.2 + - - +
46A ILE* 5.5 6.7 - - + -
67A GLN* 3.1 31.5 + - + +
68A ARG 5.4 3.8 - - - +
69A ILE* 5.6 7.9 - - + -
91A VAL* 3.2 21.1 - - + +
92A ILE* 4.9 2.7 - - + -
93A GLY* 3.2 33.0 - - - +
94A ASN* 5.5 3.8 - - - +
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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