Contacts of the strand formed by residues 41 - 49 (chain A) in PDB entry 1XTQ
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 ASN 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A TYR* 3.9 16.8 + - - +
39A ILE* 3.7 13.4 + - + +
40A GLU* 1.3 76.3 - - - +
42A THR* 1.3 72.5 + - - +
43A PHE* 3.1 42.2 - - + +
58A LEU 3.5 0.5 - - - +
59A VAL* 4.7 0.2 - - - +
60A ASP* 2.8 37.2 + - - +
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Residues in contact with THR 42 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LYS* 5.2 4.6 - - - -
40A GLU* 5.9 0.2 - - - +
41A ASN* 1.3 84.8 + - - +
43A PHE* 1.3 66.4 + - - +
44A THR* 4.6 5.0 - - - +
57A GLN* 3.3 36.1 - - + +
58A LEU 3.2 11.7 - - - +
59A VAL* 4.0 21.0 - - + +
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Residues in contact with PHE 43 (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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23A THR* 3.9 15.7 - - + -
24A ILE* 3.5 34.5 - - + -
27A VAL* 3.8 36.6 - - + -
28A GLU* 4.6 11.2 - - - -
35A TYR* 3.5 18.4 - + - -
41A ASN* 3.1 29.6 - - + +
42A THR* 1.3 76.0 - - - +
44A THR* 1.3 60.4 + - - +
56A LEU 3.7 0.2 - - - +
57A GLN* 3.4 4.9 - - - -
58A LEU* 2.8 43.2 + - + +
60A ASP* 3.9 22.0 - - + -
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Residues in contact with THR 44 (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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27A VAL* 3.9 13.9 - - - +
42A THR 4.6 4.5 - - - +
43A PHE* 1.3 77.2 - - - +
45A LYS* 1.3 63.6 + - - +
56A LEU 3.2 4.5 - - - -
57A GLN* 2.9 31.2 - - - +
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A PHE* 3.6 39.6 + - + -
27A VAL* 3.1 33.5 + - + +
28A GLU 5.8 0.2 - - - -
29A GLY 5.7 0.4 - - - +
44A THR* 1.3 76.5 - - - +
46A LEU* 1.3 69.2 + - - +
47A ILE* 3.6 27.8 - - + -
54A TYR 3.7 1.2 - - - +
55A HIS* 3.8 1.2 - - - -
56A LEU* 2.8 44.8 + - + +
58A LEU* 4.3 12.3 - - + -
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A LYS* 1.3 82.6 + - - +
47A ILE* 1.3 76.0 + - - +
48A THR* 4.9 3.8 - - + +
53A GLU* 3.4 37.2 - - + +
54A TYR 3.2 17.7 - - - +
55A HIS* 3.7 16.4 - - + +
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Residues in contact with ILE 47 (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 PHE* 3.6 32.3 - - + -
45A LYS* 3.6 16.2 - - + -
46A LEU* 1.3 87.0 - - - +
48A THR* 1.3 59.7 + - - +
49A VAL* 3.7 13.6 + - + -
53A GLU* 4.7 0.4 - - - -
54A TYR* 2.8 41.1 + - + +
56A LEU* 3.5 17.5 - - + -
160A PHE 5.2 0.2 - - - +
161A ARG* 5.0 8.5 - - + -
164A ILE* 3.2 32.5 - - + -
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Residues in contact with THR 48 (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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46A LEU* 4.9 4.2 - - + +
47A ILE* 1.3 73.4 - - - +
49A VAL* 1.3 62.0 + - - +
50A ASN 4.2 0.9 + - - -
51A GLY* 3.9 19.1 + - - -
52A GLN 3.3 9.8 + - - -
53A GLU* 4.1 12.2 + - - +
161A ARG* 5.1 4.2 + - - -
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Residues in contact with VAL 49 (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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47A ILE* 3.7 30.9 + - + -
48A THR* 1.3 76.6 - - - +
50A ASN* 1.3 87.0 + - - +
51A GLY 3.2 0.4 - - - -
52A GLN* 2.7 30.1 + - - +
54A TYR* 3.8 18.3 - - + -
161A ARG* 3.8 39.3 - - + +
164A ILE* 4.3 8.1 - - + -
165A LEU* 4.3 15.5 - - + -
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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