Contacts of the strand formed by residues 43 - 49 (chain T) in PDB entry 5A0Q
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 HIS 43 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40T SER 3.0 27.4 + - - -
42T THR* 1.3 113.8 + - - +
44T ALA* 1.4 59.7 + - - +
137T TYR* 4.6 1.1 - - - -
142T PRO* 4.6 0.4 - - - -
184T LEU* 3.0 48.6 - - + +
187T LEU* 3.6 9.0 - - - +
214T ILE* 3.3 8.5 - - + -
215T VAL 3.1 20.4 - - - +
216T GLY* 3.3 14.9 - - - -
217T LYS 4.8 0.4 - - - -
218T ASP* 4.3 15.2 - - + +
219T LEU* 3.4 26.6 - - + +
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Residues in contact with ALA 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38T LEU 4.1 4.3 - - - -
39T LYS* 4.1 9.2 - - + -
40T SER 4.4 0.2 + - - -
43T HIS* 1.4 73.1 - - - +
45T VAL* 1.3 63.1 + - - +
46T LEU 4.2 0.7 - - - -
135T ALA* 4.2 17.0 - - + -
136T GLY 4.1 16.4 - - - +
142T PRO* 4.3 10.8 - - + +
144T ILE* 4.8 3.4 - - + -
213T GLY 4.4 1.6 - - - -
214T ILE* 3.6 12.6 - - - +
215T VAL* 3.0 38.4 + - + +
221T PHE* 5.6 0.2 - - + -
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Residues in contact with VAL 45 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36T VAL 3.7 0.7 - - - +
37T GLY* 3.3 6.1 - - - -
38T LEU* 2.9 56.5 + - + +
43T HIS 3.9 1.1 - - - +
44T ALA* 1.3 81.3 - - - +
46T LEU* 1.4 64.0 + - - +
47T VAL* 3.7 17.7 - - + -
135T ALA* 5.1 2.2 - - - +
144T ILE* 5.4 0.3 - - - +
184T LEU* 3.7 12.8 - - + -
187T LEU* 3.4 37.7 - - + -
188T VAL* 3.7 21.3 - - + -
212T ILE* 4.9 0.4 - - + -
213T GLY 3.8 1.6 - - - -
214T ILE* 4.1 2.5 - - + -
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Residues in contact with LEU 46 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36T VAL 3.7 6.1 - - - +
37T GLY* 4.8 3.8 - - - -
44T ALA 4.2 0.2 - - - -
45T VAL* 1.4 75.7 - - - +
47T VAL* 1.4 64.1 + - - +
63T ILE* 3.8 34.1 - - + -
71T GLY 3.6 18.4 - - - +
72T ILE 3.8 12.6 - - - +
73T SER* 3.6 19.7 - - - +
133T LEU* 3.8 15.7 - - + +
135T ALA* 3.7 26.6 - - + +
144T ILE* 6.3 0.4 - - + -
212T ILE* 3.6 7.1 - - - +
213T GLY 2.9 33.1 + - - +
221T PHE* 3.7 16.8 - - + -
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Residues in contact with VAL 47 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35T THR* 2.9 3.9 + - - -
36T VAL* 2.9 44.4 + - + +
38T LEU* 4.4 3.8 - - + -
45T VAL* 3.7 20.4 - - + -
46T LEU* 1.4 78.7 - - - +
48T ALA* 1.4 63.5 + - - +
63T ILE* 4.5 0.7 - - - -
188T VAL* 5.5 0.9 - - - -
191T GLY* 4.2 30.5 - - - +
192T LEU* 4.4 8.7 - - + -
195T LEU* 4.3 20.0 - - + -
210T VAL* 4.5 1.3 - - + -
211T SER 3.6 11.2 - - - +
212T ILE* 4.2 17.9 - - + -
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Residues in contact with ALA 48 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35T THR* 3.5 20.0 - - - +
47T VAL* 1.4 74.4 - - - +
49T LEU* 1.3 59.9 + - - +
50T LYS 3.0 8.0 + - - -
62T LYS* 4.0 20.9 - - + -
63T ILE* 3.8 24.2 - - + -
73T SER* 4.8 0.4 - - - -
195T LEU* 4.6 4.0 - - - -
209T ASN 3.4 1.8 - - - +
210T VAL* 3.6 0.7 - - - -
211T SER* 3.1 31.4 + - - +
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Residues in contact with LEU 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T SER* 3.2 29.3 - - - +
34T ALA* 3.0 23.5 + - + +
48T ALA* 1.3 67.2 - - - +
50T LYS* 1.3 71.2 - - - +
62T LYS* 3.4 6.5 - - - +
195T LEU* 3.5 41.6 - - + +
209T ASN* 3.2 35.4 - - + +
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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