Contacts of the strand formed by residues 57 - 62 (chain D) in PDB entry 6KTR
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 SER 57 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48D TYR* 2.9 34.3 + - - -
55D LEU 5.5 0.3 + - - -
56D SER* 1.3 77.1 - - - +
58D CYS* 1.3 60.5 + - - +
59D PHE* 4.3 3.6 - - - -
70D CYS* 5.6 0.2 - - - +
71D ALA 3.8 8.2 - - - +
72D ARG* 4.0 22.9 - - - +
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Residues in contact with CYS 58 (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 TYR* 3.6 2.6 - - - -
49D THR* 2.8 55.0 + - + +
50D SER* 5.5 0.7 - - - -
51D GLY 5.7 0.4 - - - +
57D SER* 1.3 75.4 - - - +
59D PHE* 1.3 62.9 + - - +
60D LEU 4.1 0.2 + - - -
70D CYS* 2.0 51.1 - - + -
71D ALA 3.6 3.1 - - - -
145D LEU* 3.5 23.3 - - - -
162D LEU* 4.8 6.5 - - + -
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Residues in contact with PHE 59 (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 HIS* 4.0 17.0 - - + -
47D LEU 3.4 13.0 - - - -
48D TYR* 3.7 34.8 - + + -
57D SER* 4.7 2.7 - - - -
58D CYS* 1.3 78.2 - - - +
60D LEU* 1.3 64.2 + - - +
61D ARG 3.1 2.4 + - - -
69D ASP 3.4 2.8 - - - +
70D CYS* 3.6 1.0 - - - -
71D ALA* 2.8 40.4 + - + +
72D ARG 3.8 6.1 - - - -
73D GLY* 3.5 40.6 - - - +
74D GLN* 3.6 33.0 - - + -
78D SER* 4.3 7.9 - - - -
168D MET* 4.3 13.5 - - + -
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Residues in contact with LEU 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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47D LEU* 3.0 35.4 + - + +
58D CYS 4.1 1.0 + - - -
59D PHE* 1.3 67.9 - - - +
61D ARG* 1.3 60.2 + - - +
62D ILE* 3.8 25.6 - - + -
68D VAL* 4.0 9.2 - - + -
78D SER* 3.3 25.0 - - - +
80D LEU* 4.1 15.4 - - + +
101D LEU* 3.9 32.8 - - + -
109D MET* 6.3 0.2 - - + -
143D VAL* 4.3 9.0 - - + -
145D LEU* 4.0 22.0 - - + +
165D PHE* 4.0 23.7 - - + -
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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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59D PHE 3.1 2.4 + - - -
60D LEU* 1.3 74.4 - - - +
62D ILE* 1.3 63.9 + - - +
63D ARG* 4.1 17.9 - - + +
67D VAL 3.8 0.7 - - - +
68D VAL* 3.2 9.2 - - - +
69D ASP* 3.1 60.6 + - - +
70D CYS 3.4 9.3 + - - -
71D ALA* 3.7 24.8 - - + +
75D SER* 4.2 4.9 + - - -
77D HIS* 3.6 23.8 - - + +
78D SER* 4.0 3.6 - - - +
303D SO4 3.2 32.7 + - - -
304D SO4 2.9 40.8 + - - -
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Residues in contact with ILE 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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60D LEU* 3.8 14.6 + - + -
61D ARG* 1.3 75.0 - - - +
63D ARG* 1.3 66.7 + - - +
67D VAL 3.9 3.1 - - - +
68D VAL* 4.1 10.8 - - + -
77D HIS* 2.9 25.9 + - - +
80D LEU* 4.0 12.8 - - + -
92D ILE* 4.9 1.1 - - + +
93D LYS 4.5 0.7 - - - -
94D GLY* 3.6 28.3 - - - +
97D SER* 3.4 29.3 - - - +
99D ARG* 3.9 20.4 - - + +
101D LEU* 4.1 26.2 - - + +
111D GLY* 4.0 14.8 - - - -
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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