Contacts of the strand formed by residues 97 - 102 (chain A) in PDB entry 3K6R
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 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A HIS 3.4 2.4 - - - +
93A VAL* 3.3 5.7 - - - -
94A GLU 2.9 37.1 + - - +
95A ASN* 3.8 7.6 - - + +
96A GLY* 1.3 79.1 - - - +
98A LYS* 1.3 66.6 + - - +
99A TYR* 3.4 41.3 + - + +
141A LEU* 3.8 14.6 - - + -
142A PRO* 3.9 16.8 - - + -
145A VAL* 3.7 35.9 - - + -
146A TYR* 3.8 19.5 - - + -
171A ASN* 3.6 9.0 - - - +
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Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 3.8 22.9 - - + -
92A HIS 3.7 2.7 - - - -
93A VAL* 4.3 17.4 - - + +
96A GLY 4.0 4.7 + - - +
97A ILE* 1.3 75.0 - - - +
99A TYR* 1.3 61.3 + - - +
100A LYS 4.0 0.9 - - - -
141A LEU* 3.9 0.9 - - - +
167A ASN* 3.6 8.0 - - - +
170A LEU* 4.2 36.5 + - + +
171A ASN* 2.7 43.1 + - - +
172A LYS* 6.4 0.2 - - - +
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Residues in contact with TYR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A THR 3.8 0.5 - - - +
91A VAL* 3.5 1.9 - - - +
92A HIS* 2.8 46.9 + + + +
94A GLU* 4.1 19.8 + - + -
97A ILE* 3.4 35.5 - - + +
98A LYS* 1.3 71.5 - - - +
100A LYS* 1.3 63.8 + - - +
101A LEU* 3.8 5.1 + - + +
108A PHE* 3.8 28.5 - + + -
116A ARG* 3.7 11.6 - - - +
136A ILE* 3.7 23.1 - - + -
137A GLY 3.9 3.4 - - - -
138A HIS* 3.4 31.1 + - - -
141A LEU* 3.8 22.2 - - + -
142A PRO* 3.5 17.7 - - - +
167A ASN* 3.8 3.6 - - - +
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A VAL* 3.7 23.1 - - + -
90A THR 3.2 13.7 - - - +
91A VAL* 3.9 22.4 - - + +
98A LYS 4.0 0.4 - - - -
99A TYR* 1.3 74.2 - - - +
101A LEU* 1.3 65.8 + - - +
136A ILE* 3.7 2.1 - - - +
163A PHE* 3.5 22.1 - - + +
166A GLU* 2.8 32.4 + - + +
167A ASN* 2.7 36.7 + - - +
170A LEU* 4.0 12.6 - - + -
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 4.3 12.3 - - + -
89A VAL* 3.4 4.7 - - - +
90A THR* 3.0 31.4 + - + +
92A HIS* 5.9 0.4 - - + -
99A TYR* 4.4 7.0 - - + +
100A LYS* 1.3 78.6 - - - +
102A ASP* 1.3 60.3 + - - +
103A VAL* 3.2 39.3 - - + +
106A ILE* 4.3 15.5 - - + +
108A PHE* 3.4 38.6 - - + -
136A ILE* 4.0 23.1 - - + -
163A PHE* 3.7 15.9 - - - -
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Residues in contact with ASP 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A THR* 2.7 31.5 + - - -
89A VAL* 4.4 6.9 - - + +
101A LEU* 1.3 73.5 - - - +
103A VAL* 1.3 57.8 + - - +
104A ALA* 3.1 10.4 + - - +
105A LYS* 3.0 18.4 + - + +
106A ILE* 2.8 34.9 + - + +
159A TYR* 2.6 44.9 + - + +
163A PHE* 3.8 11.3 - - + -
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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