Contacts of the strand formed by residues 45 - 49 (chain B) in PDB entry 3SRF
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 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B ASN 3.6 0.4 + - - -
44B THR* 1.3 75.6 - - - +
46B ILE* 1.3 60.1 + - - +
69B ASN* 3.8 4.3 - - - -
356B ASP 3.0 12.7 + - - -
357B CYS* 3.7 22.2 - - - -
358B ILE* 3.0 28.8 + - - +
463B HIS 4.2 3.1 + - - -
535B GOL 3.3 19.0 + - - -
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 3.5 32.3 - - - +
44B THR 4.3 1.6 - - - +
45B GLY* 1.3 79.4 - - - +
47B ILE* 1.3 63.8 + - - +
48B CYS* 3.7 25.0 + - - -
67B GLY 3.7 15.5 - - - +
68B MET* 4.3 1.3 - - - -
69B ASN* 3.0 35.4 + - - +
70B VAL* 3.0 8.3 + - - +
357B CYS* 4.8 0.4 - - - +
358B ILE* 3.6 8.1 - - + -
374B VAL* 4.0 12.1 - - + +
377B GLN* 3.6 29.6 - - + +
378B HIS* 3.7 26.0 - - + +
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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
----------------------------------------------------------
46B ILE* 1.3 74.0 - - - +
48B CYS* 1.3 62.2 + - - +
70B VAL* 3.2 40.6 - - + +
72B ARG* 3.8 20.4 - - + -
240B PHE* 4.0 10.3 - - + -
324B ILE* 3.6 46.4 - - + -
357B CYS* 3.8 19.1 - - + -
358B ILE 3.1 6.8 + - - +
359B MET* 3.4 21.1 - - + +
360B LEU* 3.0 27.2 + - - +
464B LEU* 5.0 2.0 - - + -
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Residues in contact with CYS 48 (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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46B ILE* 3.7 17.3 - - - -
47B ILE* 1.3 72.4 - - - +
49B THR* 1.3 63.3 + - - +
50B ILE* 3.7 6.3 + - + +
63B MET* 4.8 2.2 - - - -
68B MET* 3.5 34.5 - - - -
70B VAL 2.8 6.7 + - - -
71B ALA* 3.3 7.3 - - - -
72B ARG 2.9 20.0 + - - -
360B LEU* 3.8 3.8 - - - +
364B THR* 3.8 19.5 - - + +
374B VAL* 3.5 31.4 - - - -
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Residues in contact with THR 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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48B CYS* 1.3 71.6 - - - +
50B ILE* 1.3 60.8 + - - +
51B GLY 3.9 0.2 - - - -
54B SER* 3.7 0.3 + - - -
72B ARG* 3.1 57.6 + - + +
74B ASN* 5.6 3.4 - - - -
359B MET* 4.5 2.7 - - + -
360B LEU 3.0 19.7 + - - +
361B SER* 3.2 23.2 - - - -
362B GLY 3.6 0.3 + - - -
364B THR* 2.7 22.8 + - - -
365B ALA* 3.3 25.7 + - - +
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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