Contacts of the strand formed by residues 90 - 99 (chain B) in PDB entry 1K4R
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 THR 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B GLU* 2.8 48.1 + - + +
85B GLU 5.0 0.2 - - - -
87B GLN* 3.1 18.3 + - + +
88B GLY 3.4 6.9 - - - +
89B GLY* 1.3 84.0 + - - +
91B VAL* 1.3 67.0 + - - +
92B CYS* 4.1 7.6 + - - -
116B CYS* 4.8 0.4 - - - -
117B VAL 3.1 11.4 - - - +
118B LYS* 3.9 20.0 - - + -
119B ALA 4.3 0.4 - - - +
238B ALA* 5.7 0.3 - - - +
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B THR* 1.3 77.3 - - - +
92B CYS* 1.3 65.7 + - - +
116B CYS* 3.2 1.6 - - - -
117B VAL* 2.8 42.0 + - + +
119B ALA* 3.9 11.2 - - + -
238B ALA* 3.6 33.0 - - + +
239B GLU* 3.9 34.1 - - + +
242B VAL* 4.5 10.3 - - + +
244B PHE* 3.7 22.8 - - + -
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Residues in contact with CYS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B GLU* 3.7 29.6 - - + +
90B THR* 4.1 10.7 - - - -
91B VAL* 1.3 78.9 - - - +
93B LYS* 1.3 62.8 + - - +
94B ARG* 5.8 1.3 - - + -
114B VAL* 4.5 3.6 - - + -
115B ALA 3.1 4.9 - - - +
116B CYS* 2.0 47.3 - - - -
244B PHE* 4.1 6.2 - - - -
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Residues in contact with LYS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B CYS* 1.3 74.5 - - - +
94B ARG* 1.3 73.2 + - - +
95B ASP* 4.3 20.8 + - - +
114B VAL* 3.3 2.9 - - - -
115B ALA 2.9 30.7 + - - -
244B PHE* 3.6 49.8 + - + +
245B GLY 5.7 1.6 + - - +
252B MET* 3.4 12.2 - - + +
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Residues in contact with ARG 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B PRO* 3.7 13.9 - - - +
80B ALA 2.8 32.9 + - - +
81B THR* 4.4 3.0 - - - +
85B GLU* 2.9 39.2 + - - +
92B CYS* 5.8 1.8 - - + -
93B LYS* 1.3 83.5 - - - +
95B ASP* 1.3 64.6 + - - +
112B SER* 3.5 18.0 + - - -
113B ILE 3.4 6.0 + - - +
114B VAL* 3.8 13.2 - - + +
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Residues in contact with ASP 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LYS* 4.1 19.9 + - - +
94B ARG* 1.3 77.4 - - - +
96B GLN* 1.3 82.1 + - - +
112B SER* 3.9 3.6 + - - -
113B ILE* 2.8 35.3 + - + +
245B GLY 5.2 0.5 - - - +
246B ALA* 5.3 0.3 - - - -
247B PRO* 3.5 26.5 - - + +
252B MET* 4.3 10.9 - - - +
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Residues in contact with GLN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASP* 1.3 90.0 + - - +
97B SER* 1.3 59.2 + - - +
110B LYS* 3.9 43.5 + - + +
111B GLY 3.2 14.8 - - - +
112B SER* 4.9 2.5 - - - -
113B ILE* 4.0 3.6 - - - -
247B PRO* 3.4 13.7 - - - +
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Residues in contact with SER 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLN* 1.3 73.8 - - - +
98B ASP* 1.3 64.0 + - - +
99B ARG* 3.5 10.9 + - - +
110B LYS* 3.4 6.3 - - - +
111B GLY 2.8 35.6 + - - -
112B SER 5.2 0.3 + - - -
113B ILE* 4.0 8.8 - - - +
247B PRO* 4.2 20.4 - - - -
249B ALA* 2.7 39.2 + - - -
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Residues in contact with ASP 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B SER* 1.3 72.5 - - - +
99B ARG* 1.3 68.4 + - - +
103B ASN* 3.8 9.9 + - - -
109B GLY 3.7 5.7 - - - +
110B LYS* 2.8 35.4 + - - +
247B PRO 5.6 0.8 + - - -
248B HIS* 5.9 0.4 - - - +
249B ALA* 3.9 9.8 + - - +
7C GLU* 4.6 27.7 - - + +
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Residues in contact with ARG 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ALA* 3.8 21.8 + - - +
73B ARG 3.6 23.8 + - - +
74B CYS* 3.9 4.2 - - - -
75B PRO* 3.8 8.1 - - + -
97B SER* 3.5 22.4 + - - +
98B ASP* 1.3 84.9 - - - +
100B GLY* 1.3 57.8 + - - +
103B ASN* 2.8 47.5 + - - +
104B HIS 4.9 0.2 - - - -
105B CYS* 3.3 26.8 - - - -
107B LEU 4.0 0.9 - - - -
108B PHE* 3.3 4.9 - - - +
109B GLY 2.8 32.4 + - - +
111B GLY* 4.0 15.5 - - - -
112B SER 5.2 0.2 + - - -
249B ALA 3.8 6.3 - - - -
250B VAL* 3.6 20.5 - - - +
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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