Contacts of the strand formed by residues 95 - 104 (chain B) in PDB entry 4KZZ
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 ASN 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B TYR* 3.7 0.4 - - - -
32B ASP* 4.3 14.6 - - - +
34B LYS* 4.5 20.7 - - - +
91B VAL* 3.7 0.7 - - - +
92B GLN* 2.6 50.4 + - + +
93B GLY 4.3 3.3 - - - +
94B LYS* 1.3 88.8 - - - +
96B CYS* 1.3 66.8 + - - +
97B LEU* 5.3 8.2 - - + +
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Residues in contact with CYS 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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31B TYR* 3.8 19.3 - - + -
32B ASP 3.8 9.2 + - - +
33B VAL* 4.0 7.6 - - + -
34B LYS* 2.9 28.9 + - - +
62B LEU* 3.1 41.1 - - + -
88B THR* 3.6 19.3 - - + +
90B ASP 3.3 4.0 - - - -
91B VAL* 3.5 8.7 - - - -
95B ASN* 1.3 81.8 - - - +
97B LEU* 1.3 63.6 + - - +
98B THR* 3.7 4.9 + - + +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LYS* 3.5 35.2 - - + -
88B THR* 4.6 0.2 - - - +
89B GLU* 2.9 26.0 + - - +
90B ASP* 2.8 20.5 + - + +
92B GLN* 4.3 23.1 - - + +
95B ASN* 5.3 6.7 - - + +
96B CYS* 1.3 75.7 - - - +
98B THR* 1.3 62.1 + - - +
228B LEU* 3.8 13.2 - - + -
229B MET* 5.4 8.5 - - - -
232B HIS* 3.2 47.1 + - + +
233B GLY* 4.9 2.9 - - - +
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Residues in contact with THR 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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33B VAL* 3.9 21.8 - - + -
34B LYS 2.5 27.9 + - - +
35B ALA* 3.7 6.6 - - - -
36B PRO* 3.3 8.7 - - - +
44B ILE* 4.0 1.2 - - - +
67B PHE* 5.6 0.9 - - + -
86B LEU* 3.8 22.4 - - + +
87B ILE 3.1 11.2 - - - +
88B THR* 3.7 26.0 - - - +
96B CYS 3.9 4.9 - - - +
97B LEU* 1.3 77.7 - - - +
99B ASN* 1.3 59.9 + - - +
232B HIS* 2.5 30.1 + - - -
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Residues in contact with ASN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PRO* 4.0 2.8 - - - +
86B LEU* 3.8 6.0 - - - -
87B ILE* 2.9 33.7 + - + +
89B GLU* 3.8 25.3 + - + +
98B THR* 1.3 74.0 - - - +
100B PHE* 1.3 84.0 + - - +
101B HIS 3.2 0.5 + - - -
133B TYR* 4.4 14.0 + - - -
181B LEU* 4.7 6.0 - - - +
182B LYS* 4.3 0.9 + - - -
227B LYS 5.7 0.2 - - - -
228B LEU* 3.2 33.8 - - + +
231B LEU* 3.9 22.9 - - - +
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Residues in contact with PHE 100 (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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36B PRO* 4.2 8.2 - - + +
39B PHE* 5.2 5.6 - + + -
84B PHE* 4.0 25.8 - + + -
85B LYS 4.0 3.6 - - - -
86B LEU* 4.6 5.8 - - + -
87B ILE* 4.3 5.5 - - - +
99B ASN* 1.3 87.2 + - - +
101B HIS* 1.3 61.6 + - - +
102B GLY* 3.7 37.2 - - - -
103B MET* 4.0 3.8 - - + -
135B LEU* 5.1 0.2 - - + -
181B LEU* 3.2 46.2 - - + +
182B LYS* 5.9 2.0 - - - +
184B VAL* 5.6 2.0 - - + -
185B VAL* 4.0 27.1 - - + -
188B LEU* 4.9 8.3 - - + -
215B VAL* 4.0 24.7 - - + -
217B MET* 4.0 16.7 - - - +
220B LYS* 5.7 0.5 - - - -
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Residues in contact with HIS 101 (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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66B VAL* 4.4 6.2 - - + +
85B LYS* 2.7 41.5 + - + +
87B ILE* 2.6 56.5 - - + +
100B PHE* 1.3 72.1 - - - +
102B GLY* 1.3 59.1 + - - +
215B VAL 4.6 0.2 - - - +
216B LYS* 5.2 0.2 - - - -
217B MET* 3.2 36.2 + - + +
220B LYS* 3.4 20.7 + - - -
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Residues in contact with GLY 102 (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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84B PHE* 3.2 5.9 - - - +
85B LYS* 2.8 41.2 + - - +
100B PHE* 3.7 19.5 - - - -
101B HIS* 1.3 80.5 - - - +
103B MET* 1.3 60.9 + - - +
215B VAL 3.4 14.4 - - - -
217B MET* 5.0 0.2 - - - -
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Residues in contact with MET 103 (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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82B ARG* 4.2 23.6 - - + -
83B LYS 3.0 11.4 - - - +
84B PHE* 4.1 16.8 - - + -
85B LYS* 4.8 1.3 - - - +
100B PHE* 4.0 7.3 - - + -
102B GLY* 1.3 76.7 - - - +
104B ASP* 1.3 71.1 + - - +
105B LEU* 4.7 2.7 - - + -
188B LEU* 4.2 22.7 - - + -
212B VAL* 2.9 47.6 - - + +
213B ARG* 3.5 14.8 - - - +
214B LYS* 3.0 16.9 - - - +
215B VAL* 2.8 41.0 + - + +
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Residues in contact with ASP 104 (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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68B GLU* 4.7 5.3 + - - +
82B ARG* 3.5 4.7 - - - -
83B LYS* 3.0 40.0 + - + +
85B LYS* 5.6 9.2 - - + +
103B MET* 1.3 82.3 - - - +
105B LEU* 1.3 92.2 + - - +
106B THR* 3.8 13.0 + - - +
110B MET* 5.4 0.7 - - - +
213B ARG* 3.6 13.4 + - - +
214B LYS* 4.5 20.1 - - + +
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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