Contacts of the strand formed by residues 35 - 40 (chain A) in PDB entry 1XZ0
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 LEU 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A TRP* 3.6 2.5 - - - -
32A LEU* 3.0 39.5 + - + +
34A ASP* 1.3 77.4 - - - +
36A GLN* 1.3 72.9 + - - +
37A THR* 4.0 3.9 - - + +
51A TRP* 4.0 20.9 - - + +
53A TRP* 3.8 28.9 - - + -
180A HIS* 4.1 19.1 - - + -
181A LEU* 4.1 15.3 - - + -
241A GLY* 6.1 5.4 - - - -
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Residues in contact with GLN 36 (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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29A SER* 3.8 12.3 - - - -
30A GLY 3.7 11.0 - - - +
31A TRP* 3.3 34.2 - - + -
35A LEU* 1.3 77.4 - - - +
37A THR* 1.3 63.0 + - - +
38A HIS 3.3 18.4 + - - +
39A THR* 3.6 8.9 + - - +
50A LEU* 3.6 20.5 - - + +
51A TRP* 3.2 21.3 + - - -
53B ASP* 2.6 47.8 + - - +
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Residues in contact with THR 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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10A PHE* 3.6 14.2 - - - -
30A GLY 3.0 7.0 + - - -
32A LEU* 4.3 12.8 - - + -
35A LEU* 4.0 10.3 - - + +
36A GLN* 1.3 79.3 - - - +
38A HIS* 1.3 92.6 + - - +
50A LEU* 3.2 22.3 + - - -
51A TRP* 4.1 15.0 - - + +
53A TRP* 4.1 19.5 - - + -
54A SER* 3.0 22.6 + - - -
173A LEU* 4.9 4.3 - - + -
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Residues in contact with HIS 38 (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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10A PHE* 4.0 11.2 - + - -
29A SER* 3.4 1.0 - - - -
30A GLY* 3.2 28.2 + - - +
36A GLN* 3.3 16.7 + - - +
37A THR* 1.3 112.0 + - - +
39A THR* 1.3 63.7 + - - +
47A ILE* 4.3 10.5 - - + -
48A VAL 3.5 7.0 - - - +
49A PHE* 4.0 20.9 - + - -
50A LEU* 4.0 1.5 - - - +
54A SER* 3.1 29.2 + - - -
63A TRP* 3.9 14.0 - + - -
169A PHE* 3.8 19.3 - + - -
173A LEU* 4.5 1.6 - - + -
601A JH0 3.9 20.6 - - + -
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Residues in contact with THR 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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28A VAL 4.0 12.3 - - - +
29A SER* 4.5 2.0 - - - +
36A GLN* 3.6 10.5 + - - +
38A HIS* 1.3 75.9 + - - +
40A TRP* 1.3 67.7 + - - +
41A ASP* 4.1 0.4 - - - -
47A ILE* 3.6 4.7 - - - +
48A VAL* 2.7 44.9 + - - +
50A LEU* 3.9 17.2 - - - +
601A JH0 5.6 2.9 - - - -
53B ASP* 3.9 19.4 + - - +
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Residues in contact with TRP 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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26A ASN* 5.8 3.4 - - - -
28A VAL* 3.3 44.6 + - + +
39A THR* 1.3 80.0 - - - +
41A ASP* 1.3 59.6 + - - +
42A SER* 3.8 28.0 + - - +
45A SER* 3.7 35.7 - - - -
46A THR* 3.6 27.6 - - - -
47A ILE* 4.1 16.8 - - + -
67A GLU* 3.8 12.1 - - + -
70A PHE* 3.6 25.8 - + + -
71A ARG* 3.5 32.5 - - + -
74A THR* 4.4 14.7 + - + -
601A JH0 5.9 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