Contacts of the strand formed by residues 85 - 92 (chain B) in PDB entry 3KDO
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 TRP 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B PHE 3.5 0.5 - - - +
30B ARG* 3.3 4.4 - - - +
31B VAL* 2.6 37.8 + - - +
33B PRO* 4.7 5.3 - - + +
39B ILE* 3.3 53.8 - - + +
40B GLU* 6.0 0.4 - - - -
77B PHE* 4.0 20.2 - - + -
78B HIS* 3.3 14.6 - - - -
79B ASP* 3.3 52.7 - - + -
80B MET* 4.4 0.2 - - - -
83B GLY* 4.5 7.9 + - - -
84B SER* 1.3 83.3 - - - +
86B ILE* 1.3 65.2 + - - +
87B VAL* 3.8 5.1 + - + -
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Residues in contact with ILE 86 (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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28B VAL* 3.7 21.1 - - + -
29B PHE 3.3 1.1 - - - +
30B ARG* 3.8 32.3 - - + +
76B ASP* 3.6 6.5 - - - +
77B PHE* 3.6 0.9 - - - -
78B HIS* 2.8 43.4 + - + +
80B MET* 3.5 26.5 - - - -
85B TRP* 1.3 71.6 - - - +
87B VAL* 1.3 62.7 + - - +
88B ARG* 4.2 6.9 + - + +
124B GLU* 4.6 2.0 - - + +
349B VAL* 3.3 31.0 - - + +
350B PHE* 3.9 24.7 - - + -
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA 3.6 1.6 - - - +
28B VAL* 4.7 0.2 - - - -
29B PHE* 2.6 43.2 + - + +
31B VAL* 3.9 23.1 - - + -
39B ILE* 4.0 22.2 - - + -
43B ALA* 3.9 20.6 - - + -
74B ALA* 4.0 18.2 - - + -
76B ASP 3.3 7.6 - - - +
77B PHE* 4.0 17.3 - - + -
85B TRP* 4.2 2.9 - - + -
86B ILE* 1.3 78.6 - - - +
88B ARG* 1.3 64.6 + - - +
89B ILE* 4.0 10.4 + - + -
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Residues in contact with ARG 88 (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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26B ILE* 4.4 3.8 - - + -
27B ALA 3.6 4.3 - - - -
28B VAL* 4.2 17.0 - - + +
74B ALA* 3.4 3.3 - - - -
75B TYR* 3.0 60.4 + - + +
76B ASP* 3.1 42.5 + - + +
78B HIS* 6.4 0.2 - - - +
86B ILE* 5.1 5.2 - - + +
87B VAL* 1.3 75.9 - - - +
89B ILE* 1.3 60.8 + - - +
348B ASP 5.2 3.2 + - - -
349B VAL* 4.6 21.8 + - - +
351B HIS 5.7 0.2 + - - -
352B LEU* 4.1 28.2 - - - +
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Residues in contact with ILE 89 (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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26B ILE* 3.4 2.8 - - - +
27B ALA 2.9 34.0 + - - +
29B PHE* 3.7 28.3 - - + -
43B ALA* 4.5 3.8 - - - +
46B VAL* 3.8 21.5 - - + -
47B ALA* 4.0 19.5 - - + +
72B ALA* 3.9 10.3 - - + -
73B LYS 3.3 16.2 - - - +
74B ALA* 4.0 10.3 - - + -
75B TYR* 4.1 2.9 - - - -
87B VAL* 4.0 11.2 - - + -
88B ARG* 1.3 80.9 - - - +
90B ALA* 1.3 62.1 + - - +
91B TYR* 3.3 30.8 - - + +
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Residues in contact with ALA 90 (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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17B TYR* 3.8 29.6 - - + -
19B PRO* 4.5 2.9 - - + -
24B ASP* 4.2 14.8 - - + +
25B ILE 3.3 4.7 - - - +
26B ILE* 4.6 1.1 - - + +
72B ALA* 3.1 8.5 - - - +
73B LYS* 2.8 33.1 + - - +
75B TYR* 3.9 17.0 - - + -
89B ILE* 1.3 71.4 - - - +
91B TYR* 1.3 63.6 + - - +
92B PRO* 4.3 1.4 - - - +
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Residues in contact with TYR 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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24B ASP* 3.4 4.2 - - - -
25B ILE* 2.6 53.0 + - + +
27B ALA* 3.8 13.0 - - + -
29B PHE* 3.9 13.0 - - - -
50B SER* 2.7 46.2 + - - -
51B SER* 4.4 4.3 - - - -
70B LEU 6.0 0.2 - - - -
72B ALA* 3.3 20.0 - - + -
89B ILE* 3.3 42.5 - - + +
90B ALA* 1.3 76.0 - - - +
92B PRO* 1.3 69.1 - - + +
95B ALA* 5.7 0.7 - - + -
96B PHE* 3.6 34.5 - + + -
108B ILE* 3.7 16.6 - - + +
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Residues in contact with PRO 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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23B ARG* 3.8 7.0 - - + +
24B ASP* 3.8 8.7 - - - +
25B ILE* 4.4 0.2 - - - -
69B ASP 3.7 18.6 - - - +
70B LEU* 3.8 23.8 - - - +
71B SER 4.1 12.6 - - - +
90B ALA 4.3 1.8 - - - +
91B TYR* 1.3 85.7 - - + +
93B PHE* 1.3 66.9 + - - +
94B HIS* 3.6 24.0 - - + -
95B ALA* 3.0 22.5 + - + +
96B PHE* 3.7 4.5 - - - -
23F ARG* 3.8 13.7 - - - +
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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