Contacts of the strand formed by residues 74 - 79 (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 VAL 74 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D PHE* 4.1 1.3 - - - -
64D VAL* 3.7 20.3 - - - +
65D GLN* 4.2 5.4 + - - +
72D GLY 3.7 10.8 - - - +
73D SER* 1.3 80.2 - - - +
75D ARG* 1.3 66.5 + - - +
76D GLU* 5.8 1.1 - - + -
89D THR* 3.6 28.9 - - + -
90D GLU 3.3 5.4 - - - +
91D VAL* 4.4 11.9 - - + -
107D VAL* 5.4 3.4 - - + -
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Residues in contact with ARG 75 (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 ARG 4.7 0.4 + - - -
49D PHE* 2.8 72.7 + - + +
52D PRO* 3.7 24.6 - - - +
56D LYS* 4.4 15.6 - - - +
59D ILE* 5.6 1.4 - - - +
62D CYS* 3.7 15.5 - - - -
63D VAL 3.3 5.2 - - - +
64D VAL* 3.5 19.1 - - + -
74D VAL* 1.3 78.0 - - - +
76D GLU* 1.3 60.7 + - - +
77D VAL* 3.9 9.6 - - + +
88D SER 3.9 0.2 - - - +
89D THR* 3.4 7.1 - - - +
90D GLU* 2.6 64.3 + - + +
102D LEU* 6.0 0.8 - - - +
104D ILE* 4.5 14.8 - - - +
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Residues in contact with GLU 76 (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* 4.2 1.0 + - - +
62D CYS* 3.5 1.4 - - - -
63D VAL* 2.9 47.6 + - + +
74D VAL* 5.8 1.3 - - + -
75D ARG* 1.3 74.1 - - - +
77D VAL* 1.3 63.0 + - - +
78D ASP* 5.2 5.6 - - - +
87D LYS* 4.4 25.8 + - - +
88D SER 3.4 15.5 + - - +
89D THR* 3.3 28.5 + - + +
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Residues in contact with VAL 77 (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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52D PRO* 5.0 2.9 - - + -
59D ILE* 4.3 16.6 - - + -
61D ARG 3.3 9.9 - - - +
62D CYS* 4.3 5.4 - - - -
75D ARG* 3.9 33.2 - - + +
76D GLU* 1.3 78.7 - - - +
78D ASP* 1.3 72.6 + - - +
79D LEU* 4.1 18.6 - - + -
87D LYS* 3.3 7.6 - - - +
88D SER* 2.8 47.9 + - - +
90D GLU* 4.1 11.0 - - - +
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Residues in contact with ASP 78 (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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59D ILE* 3.9 2.9 - - - +
60D SER* 2.9 35.2 + - - +
61D ARG* 3.0 48.0 + - + +
76D GLU* 5.2 5.0 - - - +
77D VAL* 1.3 78.7 - - - +
79D LEU* 1.3 63.7 + - - +
86D THR 3.6 6.0 - - - +
87D LYS* 3.6 24.4 + - - +
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Residues in contact with LEU 79 (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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58D PHE* 3.3 27.4 - - + +
59D ILE* 4.2 7.0 - - + -
60D SER* 4.0 5.9 + - - -
77D VAL* 4.1 19.7 - - + -
78D ASP* 1.3 78.2 - - - +
80D LYS* 1.3 71.1 + - - +
81D SER* 3.9 0.5 + - - -
83D LEU* 4.4 12.1 - - + -
85D ALA* 3.7 39.5 - - + +
86D THR* 2.9 22.0 + - - +
87D LYS* 4.7 4.0 - - - +
88D SER* 5.8 3.1 - - - -
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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