Contacts of the strand formed by residues 46 - 50 (chain B) in PDB entry 1T5A
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 46 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ARG* 4.0 3.6 - - - -
44B ASN 3.5 4.8 + - - -
45B THR* 1.3 74.5 - - - +
47B ILE* 1.3 59.7 + - - -
48B ILE* 4.1 0.9 - - - -
70B ASN* 4.1 10.1 - - - -
71B VAL* 6.4 0.2 - - - -
357B ASP 2.9 13.5 + - - -
358B CYS* 3.2 15.6 - - - -
359B ILE* 3.1 27.4 + - - +
464B HIS* 4.1 12.1 + - - -
466B TYR 5.5 0.2 + - - -
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ARG* 3.4 29.6 - - - +
45B THR 4.0 2.9 - - - +
46B GLY* 1.3 74.6 - - - +
48B ILE* 1.3 65.4 + - - +
49B CYS* 3.7 22.7 + - - -
68B GLY 4.1 4.0 - - - +
69B MET* 3.8 4.3 - - - -
70B ASN* 3.0 39.9 + - - +
71B VAL 3.4 3.1 + - - -
359B ILE* 3.7 9.4 - - + -
361B LEU* 4.8 1.8 - - + -
375B VAL* 4.0 13.2 - - + +
378B GLN* 3.5 31.2 - - + +
379B ASN* 3.6 28.7 - - + +
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 1.3 74.9 - - - +
49B CYS* 1.3 61.5 + - - +
71B VAL* 3.4 36.8 - - + +
73B ARG* 4.0 23.8 - - + -
241B PHE* 4.1 15.3 - - + -
325B ILE* 3.5 46.0 - - + -
358B CYS* 3.8 18.2 - - + -
359B ILE 3.2 7.4 + - - +
360B MET* 3.3 15.5 - - + +
361B LEU* 3.1 24.8 + - - +
465B LEU* 5.0 2.7 - - + -
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Residues in contact with CYS 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 3.8 13.2 - - - -
48B ILE* 1.3 77.9 - - - +
50B THR* 1.3 62.2 + - - +
51B ILE* 3.3 7.4 + - + +
64B MET* 4.8 1.6 - - - -
69B MET* 3.6 36.8 - - + -
71B VAL 2.9 7.3 + - - -
72B ALA* 3.5 5.7 - - - -
73B ARG* 2.8 23.1 + - - -
361B LEU* 4.0 5.8 - - - -
365B THR* 3.7 13.9 - - - +
375B VAL* 3.4 31.4 - - - -
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Residues in contact with THR 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B CYS* 1.3 71.2 - - - +
51B ILE* 1.3 68.3 + - - +
55B SER* 3.9 0.5 + - - -
73B ARG* 2.8 56.5 + - - +
75B ASN* 4.2 14.8 - - + +
360B MET* 4.4 1.2 - - - +
361B LEU 2.8 25.5 + - - -
362B SER* 3.4 13.7 + - - -
365B THR* 2.9 19.1 + - - +
366B ALA* 3.5 20.9 + - + -
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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