Contacts of the strand formed by residues 37 - 41 (chain H) in PDB entry 6CP3
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 37 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33H PRO* 4.8 0.9 - - - -
34H ALA* 2.8 32.6 + - - -
35H LYS 3.2 2.6 + - - -
36H SER* 1.3 79.3 - - - +
38H ARG* 1.3 64.9 + - - -
39H ILE* 3.4 8.6 + - - +
39L ARG* 4.3 0.9 - - - -
39M ARG* 3.3 19.7 - - - -
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Residues in contact with ARG 38 (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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31H ASN* 3.5 32.7 - - + +
32H LEU 3.7 15.0 - - - +
33H PRO* 4.3 8.3 - - + -
37H GLY* 1.3 70.7 - - - -
39H ILE* 1.3 66.5 + - - +
56H VAL* 3.9 38.9 + - - +
58H GLU* 3.7 24.2 + - - +
67H LYS* 5.0 5.5 - - - +
39L ARG* 3.7 1.6 + - - +
40L ASN* 3.3 33.1 + - - +
42L SER* 5.7 2.2 - - - -
43L ILE* 6.1 4.4 - - - +
38M SER 4.0 2.6 - - - +
39M ARG* 3.0 15.9 + - - +
41M PRO* 4.2 30.2 - - + +
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Residues in contact with ILE 39 (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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31H ASN* 4.5 1.1 - - - -
32H LEU* 2.9 39.8 + - + +
34H ALA* 4.1 4.5 - - + -
36H SER* 3.8 5.6 - - - +
37H GLY 3.5 11.9 - - - +
38H ARG* 1.3 79.5 - - - +
40H GLY* 1.3 71.2 + - - +
41H VAL* 4.3 8.7 - - + -
45H HIS* 4.7 6.5 - - - +
50H GLU* 3.5 38.6 - - - +
39K ARG* 3.9 12.1 - - - +
39L ARG* 3.4 52.0 - - - +
40L ASN* 5.0 0.4 - - - -
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Residues in contact with GLY 40 (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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29H GLN* 5.2 0.7 - - - -
30H VAL 3.1 11.9 - - - -
31H ASN* 3.3 14.1 + - - -
38H ARG 4.2 0.8 + - - -
39H ILE* 1.3 80.6 - - - +
41H VAL* 1.3 63.8 + - - +
42H LEU* 5.3 0.4 - - - -
45H HIS* 4.3 3.1 + - - -
40K ASN* 4.2 5.9 + - - -
38L SER 4.7 0.3 - - - +
39L ARG* 3.6 8.7 + - - +
40L ASN* 4.2 3.2 + - - +
41L PRO* 3.6 29.4 - - - +
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Residues in contact with VAL 41 (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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10H LEU* 4.1 11.3 - - + +
28H THR 4.0 0.7 - - - +
29H GLN* 3.7 4.3 - - - -
30H VAL* 2.8 45.8 + - + +
32H LEU* 4.7 9.4 - - + -
39H ILE* 4.3 10.3 - - + -
40H GLY* 1.3 77.2 - - - +
42H LEU* 1.3 71.6 + - - +
45H HIS* 3.5 41.5 - - + +
50H GLU* 5.3 3.4 - - - +
77H VAL* 4.8 3.8 - - + -
83H LEU* 3.7 28.5 - - + -
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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