Contacts of the strand formed by residues 45 - 49 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H ASN 3.7 2.8 + - - -
44H THR* 1.3 75.4 - - - +
46H ILE* 1.3 59.0 + - - -
69H ASN* 3.3 11.7 - - - -
356H ASP 3.0 12.5 + - - -
357H CYS* 3.6 20.4 - - - -
358H ILE* 3.0 30.5 + - - +
463H HIS* 3.9 10.2 + - - -
465H TYR 5.6 0.2 + - - -
466H ARG* 5.5 0.2 - - - +
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Residues in contact with ILE 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H ARG* 3.5 32.8 - - - +
44H THR 4.3 1.3 - - - +
45H GLY* 1.3 74.8 - - - +
47H ILE* 1.3 63.1 + - - +
48H CYS* 3.8 23.9 + - - -
67H GLY 3.9 11.2 - - - +
68H MET* 4.2 0.6 - - - -
69H ASN* 3.0 34.3 + - - +
70H VAL 3.1 7.3 + - - +
358H ILE* 3.6 9.2 - - + -
360H LEU* 4.6 0.2 - - + -
374H VAL* 3.9 19.1 - - + +
377H GLN* 3.6 26.2 - - + +
378H HIS* 3.6 28.3 - - + +
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Residues in contact with ILE 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H ILE* 1.3 73.4 - - - +
48H CYS* 1.3 63.2 + - - +
70H VAL* 3.5 34.3 - - + +
72H ARG* 4.0 22.4 - - + -
240H PHE* 3.9 16.8 - - + -
324H ILE* 3.8 33.0 - - + -
357H CYS* 3.8 29.8 - - + -
358H ILE 3.0 8.7 + - - +
359H MET* 3.3 19.9 - - + +
360H LEU* 2.8 28.1 + - - +
464H LEU* 5.0 2.9 - - + -
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Residues in contact with CYS 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H ILE* 3.8 17.7 - - - -
47H ILE* 1.3 73.8 - - - +
49H THR* 1.3 62.4 + - - +
50H ILE* 3.8 5.4 + - + +
63H MET* 5.0 2.0 - - - -
68H MET* 3.5 33.7 - - - -
70H VAL 3.0 5.7 + - - -
71H ALA* 3.4 6.6 - - - -
72H ARG* 2.8 23.0 + - - -
360H LEU* 3.7 7.9 - - - -
364H THR* 3.8 16.6 - - + +
374H VAL* 3.6 31.4 - - - -
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Residues in contact with THR 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H CYS* 1.3 71.9 - - - +
50H ILE* 1.3 61.6 + - - +
54H SER* 3.9 0.5 + - - -
72H ARG* 3.1 55.3 + - + +
74H ASN* 5.7 3.6 - - - -
359H MET* 4.2 4.3 - - + -
360H LEU 3.0 18.2 + - - +
361H SER* 3.5 18.8 - - - -
364H THR* 2.7 24.5 + - - -
365H ALA* 3.4 29.2 + - - +
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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