Contacts of the strand formed by residues 118 - 127 (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 VAL 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B VAL* 4.1 25.4 - - + -
32B THR 3.5 6.7 - - - +
34B ALA* 4.2 1.8 - - - -
42B ALA* 4.3 8.3 - - + +
46B VAL* 4.4 16.6 - - + -
112B ILE 4.1 15.9 - - - +
115B MET* 3.1 18.1 - - + +
116B LYS 3.6 4.3 - - - +
117B ARG* 1.3 86.5 - - + +
119B LYS* 1.3 52.6 + - - +
120B GLY 4.0 10.1 - - - +
121B LEU* 4.4 14.8 - - + +
290G ARG* 2.7 42.3 + - - +
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Residues in contact with LYS 119 (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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32B THR* 2.7 28.1 + - + +
33B PRO 4.5 0.7 - - - +
34B ALA* 3.9 15.2 - - + +
118B VAL* 1.3 73.4 - - - +
120B GLY* 1.3 57.5 + - - +
294B HIS* 4.8 1.9 + - - -
290G ARG* 4.4 13.7 + - - +
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Residues in contact with GLY 120 (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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30B ARG 3.7 0.9 - - - +
31B VAL* 4.0 0.7 - - - -
32B THR* 3.0 34.8 + - - +
118B VAL* 3.3 7.7 - - - +
119B LYS* 1.3 81.8 - - - +
121B LEU* 1.3 60.8 + - - +
293B TYR* 3.4 17.0 - - - -
294B HIS* 3.6 13.9 - - - -
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PHE* 3.7 26.2 - - + -
30B ARG 3.7 1.6 - - - +
31B VAL* 3.8 30.1 - - + -
46B VAL* 4.3 14.8 - - + -
112B ILE* 3.5 54.7 - - + +
113B PHE* 3.4 18.9 - - + +
115B MET* 4.7 0.2 - - + -
118B VAL* 4.4 12.6 - - + -
120B GLY* 1.3 74.4 - - - +
122B ARG* 1.3 61.6 + - - +
293B TYR 3.4 0.6 + - - -
294B HIS* 3.0 14.2 + - + +
295B GLY 2.8 20.8 + - - -
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Residues in contact with ARG 122 (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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29B PHE* 3.4 4.9 - - - -
30B ARG* 2.8 48.6 + - + -
121B LEU* 1.3 74.8 - - - +
123B LEU* 1.3 68.0 + - - +
124B GLU* 2.6 45.4 + - - +
288B PHE 5.2 0.4 + - - -
289B THR 3.2 24.9 + - - -
290B ARG 5.0 1.0 + - - -
291B ASN 3.6 12.9 + - - +
292B PRO* 3.6 22.7 + - - +
293B TYR 3.8 4.9 - - - -
294B HIS 3.5 26.4 + - - +
295B GLY 3.2 5.5 - - - -
296B ILE 4.1 2.6 - - - -
297B SER* 3.6 27.9 + - - +
298B MET 4.8 0.4 - - - +
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Residues in contact with LEU 123 (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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27B ALA* 4.1 9.6 - - + -
28B VAL 3.8 6.1 - - - +
29B PHE* 3.4 36.1 - - + -
105B LEU* 5.7 0.9 - - + -
108B ILE* 4.1 27.6 - - + +
109B ALA* 4.3 9.4 - - + -
113B PHE* 4.3 8.6 - - + -
121B LEU 4.2 0.4 - - - -
122B ARG* 1.3 69.6 - - - +
124B GLU* 1.3 59.6 + - - +
125B ASP 3.7 17.9 - - - +
126B LEU* 4.6 4.9 - - + -
295B GLY 2.8 14.9 + - - +
296B ILE* 4.3 12.6 - - + -
297B SER* 2.9 27.9 + - - -
300B VAL* 3.9 27.2 - - + +
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Residues in contact with GLU 124 (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* 2.7 21.5 + - + +
29B PHE 4.4 1.6 - - - -
30B ARG* 3.4 38.0 + - + +
86B ILE* 4.6 1.6 - - + -
122B ARG* 2.6 46.3 + - - +
123B LEU* 1.3 73.4 - - - +
125B ASP* 1.3 59.4 + - - +
292B PRO 4.0 1.7 - - - +
297B SER* 3.6 17.7 + - - -
299B PHE* 3.8 11.8 - - - +
300B VAL* 3.8 4.2 - - - +
350B PHE* 3.6 43.8 - - + +
351B HIS* 3.9 6.9 + - - -
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Residues in contact with ASP 125 (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 0.2 - - - -
27B ALA* 3.7 3.3 - - - -
28B VAL* 3.0 33.9 + - + +
123B LEU* 3.6 7.2 - - - +
124B GLU* 1.3 81.2 - - - +
126B LEU* 1.3 96.1 + - - +
127B TYR 4.2 1.6 - - - -
299B PHE* 3.8 20.8 - - - -
300B VAL* 3.8 9.2 - - - -
303B LYS* 3.4 11.7 + - - -
350B PHE 3.5 16.6 - - - +
351B HIS* 3.5 3.5 - - + -
352B LEU* 2.8 37.1 + - - +
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Residues in contact with LEU 126 (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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25B ILE* 4.2 14.4 - - + -
26B ILE 3.5 14.8 - - - +
27B ALA* 4.0 18.4 - - + -
104B LEU* 4.4 2.7 - - + -
105B LEU* 4.5 7.4 - - + -
108B ILE* 3.8 33.2 - - + -
123B LEU* 4.6 3.8 - - + -
125B ASP* 1.3 90.5 + - - +
127B TYR* 1.3 57.3 + - - +
128B PHE* 3.8 28.0 - - + -
300B VAL* 4.0 27.3 - - + +
303B LYS* 2.7 36.9 + - + +
304B LEU* 4.8 6.3 - - + -
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Residues in contact with TYR 127 (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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21B LYS* 2.5 43.5 + - + +
24B ASP 3.5 22.0 - - - -
25B ILE* 3.5 4.9 - - - +
26B ILE* 2.7 58.5 + - + +
125B ASP* 4.1 1.2 + - - +
126B LEU* 1.3 71.6 - - - +
128B PHE* 1.3 85.2 + - - +
129B PRO* 4.1 2.6 - - - +
130B GLU 5.1 0.7 + - - -
303B LYS* 4.1 1.1 - - - +
352B LEU* 4.3 17.5 - - + -
353B GLU 3.2 27.8 - - - -
354B GLN* 3.5 19.1 - - - +
355B LYS 5.4 1.6 - - - -
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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