Contacts of the strand formed by residues 370 - 376 (chain I) in PDB entry 5BRR
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 VAL 370 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13I SER* 3.2 26.6 + - - +
17I VAL* 4.9 10.5 - - + -
36I PRO* 3.4 18.3 - - + +
37I TYR* 3.2 22.9 + - - +
255I SER 5.3 0.4 - - - -
256I ALA* 4.2 17.5 - - + +
259I ILE* 4.9 10.3 - - + -
361I VAL* 3.8 23.3 - - + -
362I VAL 3.8 2.5 - - - -
363I ARG* 4.8 2.2 - - + +
368I GLY 3.9 9.2 - - - +
369I THR* 1.3 76.5 - - - +
371I LEU* 1.3 61.8 + - - +
372I PHE 3.8 18.2 - - - +
373I MET* 5.1 0.7 - - - -
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Residues in contact with LEU 371 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I SER* 2.9 27.1 + - - +
36I PRO* 3.9 1.1 - - - -
37I TYR* 4.0 23.3 - - + -
78I LEU* 5.7 0.4 - - + -
82I LEU* 3.5 28.5 - - + -
91I ILE* 4.1 13.2 - - + -
169I LEU* 5.6 2.4 - - + +
233I LEU* 3.9 37.2 - - + -
362I VAL* 3.1 11.0 + - + +
363I ARG 4.4 3.8 - - - +
364I HIS* 4.3 8.5 - - + +
369I THR* 4.0 19.7 - - + +
370I VAL* 1.3 74.3 - - - +
372I PHE* 1.3 82.9 + - + +
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Residues in contact with PHE 372 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I PHE 3.3 9.0 - - - -
35I SER* 4.2 4.9 - - - -
36I PRO* 4.0 2.5 - - - -
91I ILE* 4.0 18.8 - - + -
169I LEU* 3.7 35.0 - - + -
170I TYR 4.9 0.2 - - - -
171I PHE* 3.4 36.1 - + + -
324I VAL* 3.7 32.8 - - + -
326I ILE* 4.0 11.4 - - + -
360I PHE* 4.4 6.5 - - + -
361I VAL* 3.3 4.7 - - - -
362I VAL* 3.0 51.3 + - + +
370I VAL* 3.6 8.0 - - - +
371I LEU* 1.3 93.0 - - + +
373I MET* 1.3 65.3 + - - +
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Residues in contact with MET 373 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I VAL* 3.7 28.5 - - + -
20I PHE* 3.4 48.5 - - + -
33I VAL* 3.3 4.3 - - - +
34I PHE 3.1 29.3 + - - +
36I PRO* 3.8 19.7 - - + -
251I THR 4.3 2.2 - - - +
254I LEU* 3.2 37.5 - - + -
359I LEU* 5.7 0.7 - - + -
360I PHE* 3.3 24.7 - - - +
361I VAL* 4.0 10.3 - - + -
370I VAL* 5.1 1.3 - - - -
372I PHE* 1.3 78.1 - - - +
374I GLY* 1.3 61.1 - - - +
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Residues in contact with GLY 374 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I PHE* 3.7 11.7 - - - -
32I VAL 3.1 14.8 - - - -
359I LEU* 2.8 29.8 - - - +
360I PHE* 3.1 19.3 + - - -
373I MET* 1.3 81.4 - - - +
375I GLN* 1.3 62.3 + - - -
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Residues in contact with GLN 375 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I PHE* 4.1 13.0 - - + -
24I ALA* 3.9 24.4 + - - +
27I SER* 4.0 3.3 + - - -
28I LYS 3.7 13.4 + - - +
30I ARG 3.4 18.3 - - - +
31I ASN* 3.6 7.8 - - - +
32I VAL* 3.1 34.7 + - + +
247I LEU* 3.9 8.7 - - + +
248I SER* 4.5 11.7 - - - -
251I THR* 4.3 18.7 - - + +
280I LEU* 4.4 1.0 - - - +
358I PHE 3.5 5.4 - - - -
359I LEU* 4.1 1.3 - - - -
374I GLY* 1.3 73.1 - - - -
376I VAL* 1.3 62.7 + - - +
377I MET* 3.5 31.1 - - + +
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Residues in contact with VAL 376 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I ASN* 4.6 3.8 - - - +
189I PHE* 4.4 1.5 - - + -
278I PHE* 4.0 27.8 - - + -
280I LEU* 4.2 14.1 - - + -
357I PRO* 3.1 8.5 - - - +
358I PHE* 2.6 72.7 + - + +
360I PHE* 4.2 9.6 - - + -
374I GLY 4.1 0.2 - - - -
375I GLN* 1.3 72.8 - - - +
377I MET* 1.3 59.5 + - - +
378I GLU* 4.2 18.8 - - - +
379I PRO* 4.3 12.3 - - + -
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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