Contacts of the strand formed by residues 45 - 49 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D ARG* 3.9 0.2 - - - -
43D ASN 3.4 4.9 + - - -
44D THR* 1.3 72.1 - - - +
46D ILE* 1.3 60.3 + - - -
69D ASN* 3.4 6.7 - - - -
356D ASP 3.2 11.7 + - - -
357D CYS* 3.5 14.7 - - - -
358D ILE* 2.9 30.7 + - - +
463D HIS 4.2 0.7 - - - -
466D ARG* 5.6 0.2 - - - +
535D GOL 3.3 22.5 + - - -
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Residues in contact with ILE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ARG* 3.5 31.0 - - - +
44D THR 4.1 2.7 - - - +
45D GLY* 1.3 74.5 - - - +
47D ILE* 1.3 65.1 + - - +
48D CYS* 3.8 22.9 - - - -
67D GLY 3.5 12.6 - - - +
68D MET* 4.2 0.4 - - - -
69D ASN* 3.0 33.1 + - - +
70D VAL* 3.2 8.0 + - - +
358D ILE* 3.6 7.6 - - + -
360D LEU* 4.9 0.9 - - + -
374D VAL* 3.7 35.2 - - + +
377D GLN* 3.6 25.4 - - + +
378D HIS* 3.7 16.2 - - + +
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Residues in contact with ILE 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ILE* 1.3 78.2 - - - +
48D CYS* 1.3 66.5 + - - +
70D VAL* 3.4 30.5 - - + +
72D ARG* 3.8 23.3 - - + -
240D PHE* 4.2 13.2 - - + -
324D ILE* 3.8 43.1 - - + -
357D CYS* 3.9 15.9 - - + -
358D ILE 2.9 10.2 + - - +
359D MET* 3.7 22.2 - - + -
360D LEU* 2.9 27.6 + - - +
464D LEU* 4.9 3.4 - - + -
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Residues in contact with CYS 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ILE* 3.8 16.4 - - - -
47D ILE* 1.3 78.7 - - - +
49D THR* 1.3 59.4 + - - +
50D ILE* 3.6 7.0 - - + +
63D MET* 5.0 2.9 - - - -
68D MET* 3.7 41.5 - - - -
70D VAL 2.9 6.7 + - - -
71D ALA* 3.5 4.3 - - - -
72D ARG* 2.7 31.6 + - - -
360D LEU* 3.7 7.2 - - - -
364D THR* 3.9 12.8 - - + +
374D VAL* 3.8 21.1 - - - -
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Residues in contact with THR 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D CYS* 1.3 70.9 - - - +
50D ILE* 1.3 64.9 + - - +
54D SER* 3.7 1.4 + - - -
72D ARG* 2.5 54.7 + - - +
74D ASN* 4.6 11.7 - - + +
360D LEU 3.0 19.6 + - - -
361D SER* 3.3 11.3 - - - -
362D GLY 4.3 0.9 - - - +
364D THR* 3.0 17.2 + - - -
365D ALA* 3.3 29.7 + - + -
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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