Contacts of the strand formed by residues 77 - 83 (chain D) in PDB entry 2KI4
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 LEU 77 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D GLU* 3.5 28.0 - - + +
48D TYR* 3.3 26.0 - - + +
74D GLU* 2.7 51.6 + - + +
75D GLU 3.2 1.8 - - - +
76D CYS* 1.3 72.1 - - - +
78D PHE* 1.3 61.6 + - - +
92D SER* 3.7 3.6 - - - -
93D LYS* 3.4 44.9 + - + +
94D LYS* 4.0 12.1 + - + +
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Residues in contact with PHE 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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46D GLU* 3.3 5.0 - - - +
47D VAL* 2.6 47.4 + - + +
49D ILE* 3.3 25.6 - - + -
60D MET* 3.2 34.8 - - + -
75D GLU 3.3 13.9 - - - -
76D CYS* 2.9 38.8 - - - -
77D LEU* 1.3 74.4 - - - +
79D LEU* 1.3 58.3 + - - +
90D TYR* 3.7 19.3 - - + -
91D ILE 3.1 5.8 - - - +
92D SER* 3.2 44.9 - - - -
93D LYS 5.0 0.2 - - - -
102D VAL* 3.7 22.2 - - + -
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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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44D VAL 4.5 4.3 - - - +
45D GLY* 3.1 32.3 - - - +
46D GLU* 4.5 4.7 - - + +
47D VAL* 4.3 0.2 - - - -
78D PHE* 1.3 71.2 - - - +
80D GLU* 1.3 70.4 + - - +
81D ARG* 3.3 6.1 + - + +
89D THR 3.4 0.2 - - - +
90D TYR* 3.2 7.3 - - - -
91D ILE* 2.6 67.3 + - + +
93D LYS* 4.6 15.6 - - + +
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Residues in contact with GLU 80 (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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39D LEU* 5.8 2.9 - - - +
41D ALA* 4.9 8.1 + - - +
45D GLY* 2.6 20.2 + - - +
47D VAL* 3.3 37.1 - - + +
78D PHE 3.6 1.8 + - - -
79D LEU* 1.3 77.3 - - - +
81D ARG* 1.3 63.7 + - - +
82D LEU* 4.8 18.8 - - + +
88D ASN* 5.1 4.7 + - - +
89D THR 3.8 2.7 - - - -
90D TYR* 4.2 12.7 - - + -
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Residues in contact with ARG 81 (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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79D LEU* 3.3 8.3 + - + +
80D GLU* 1.3 75.7 - - - +
82D LEU* 1.3 85.5 + - - +
84D GLU* 5.9 0.8 + - - -
88D ASN* 4.4 0.7 - - - +
89D THR* 2.5 65.7 + - + +
91D ILE* 4.7 16.8 - - + -
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Residues in contact with LEU 82 (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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80D GLU* 4.8 14.8 - - + +
81D ARG* 1.3 111.5 + - - +
83D GLU* 1.3 62.0 + - - +
84D GLU* 4.3 3.1 + - - +
87D TYR 4.1 3.4 - - - +
88D ASN* 3.0 35.7 - - - +
89D THR* 4.4 0.9 - - - -
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Residues in contact with GLU 83 (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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82D LEU* 1.3 75.2 - - - +
84D GLU* 1.3 66.8 + - + +
85D ASN* 2.6 31.6 + - + +
86D HIS* 3.5 5.7 + - - -
87D TYR 3.2 17.6 + - - +
89D THR* 4.0 3.9 + - - +
118D TYR* 4.9 13.9 + - - -
121D LYS* 2.9 31.2 + - - -
124D LEU* 3.1 38.1 - - + +
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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