Contacts of the strand formed by residues 59 - 64 (chain D) in PDB entry 3RT0
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 ILE 59 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D PRO* 3.5 34.8 - - + -
53D GLN* 4.0 27.5 - - + +
56D LYS* 3.4 33.5 + - + +
57D PRO 3.3 1.0 - - - -
58D PHE* 1.3 81.1 - - + +
60D SER* 1.3 62.3 + - - +
61D ARG 3.5 26.9 - - - +
62D CYS* 4.6 1.1 - - + -
75D ARG* 5.6 1.3 - - - +
77D VAL* 4.3 13.9 - - + -
78D ASP 3.9 4.3 - - - +
79D LEU* 4.2 14.4 - - + -
80D LYS* 3.5 15.4 + - - -
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Residues in contact with SER 60 (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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200B SER* 5.7 0.7 + - - -
201B GLU* 5.0 13.6 + - - -
53D GLN* 5.5 3.5 - - - +
58D PHE 3.8 1.4 + - - -
59D ILE* 1.3 75.5 - - - +
61D ARG* 1.3 74.3 + - - +
78D ASP* 2.9 24.8 + - - +
79D LEU 4.0 3.3 + - - -
80D LYS* 3.6 30.1 - - - +
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Residues in contact with ARG 61 (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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53D GLN* 4.8 3.4 - - - -
59D ILE* 3.5 11.4 - - - +
60D SER* 1.3 92.9 + - - +
62D CYS* 1.3 61.3 + - - +
63D VAL* 3.1 40.6 - - - +
76D GLU 4.6 1.2 + - - -
77D VAL* 3.3 3.6 - - - -
78D ASP* 3.0 49.4 + - + +
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Residues in contact with CYS 62 (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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50D ASP* 3.7 17.1 - - - +
52D PRO* 3.5 26.9 - - + -
53D GLN* 3.7 28.7 + - - +
59D ILE* 4.6 0.7 - - + -
61D ARG* 1.3 77.2 - - - +
63D VAL* 1.3 71.3 + - - +
75D ARG* 3.7 31.2 - - - -
76D GLU 3.5 4.7 - - - -
77D VAL* 4.3 7.0 - - + +
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Residues in contact with VAL 63 (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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61D ARG* 3.1 37.9 - - - +
62D CYS* 1.3 78.8 - - - +
64D VAL* 1.3 66.8 + - - +
74D VAL 4.1 0.2 - - - +
75D ARG* 3.3 4.5 - - - -
76D GLU* 2.9 53.4 + - + +
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Residues in contact with VAL 64 (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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49D PHE* 4.2 10.1 - - + -
50D ASP* 3.9 36.1 - - + +
62D CYS* 4.9 1.3 - - - -
63D VAL* 1.3 76.2 - - - +
65D GLN* 1.3 66.2 + - - +
66D GLY 3.3 23.6 - - - +
67D LYS* 5.1 2.7 - - + -
69D LEU* 5.7 1.1 - - + -
73D SER* 5.7 3.4 - - - -
74D VAL 3.7 11.2 - - - +
75D ARG* 3.5 27.6 - - + -
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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