Contacts of the strand formed by residues 118 - 127 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290B ARG* 2.9 30.7 + - - +
31G VAL* 4.7 5.6 - - + -
32G THR 3.5 8.7 - - - +
34G ALA* 4.2 0.9 - - - -
42G ALA* 4.6 10.1 - - + -
46G VAL* 4.4 23.1 - - + -
112G ILE 4.1 9.6 - - - +
113G PHE 4.7 0.2 - - - +
115G MET* 3.0 29.2 - - + +
116G LYS 3.0 4.4 - - - +
117G ARG* 1.3 94.5 - - + +
119G LYS* 1.3 61.1 + - - +
120G GLY 4.3 11.2 - - - +
121G LEU* 4.5 12.3 - - + +
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Residues in contact with LYS 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B ARG* 4.6 12.3 + - - +
32G THR* 2.6 35.1 + - + +
33G PRO 4.1 11.2 + - - +
34G ALA* 3.8 12.1 - - + +
35G GLU* 5.3 4.2 - - - +
118G VAL* 1.3 74.2 - - - +
120G GLY* 1.3 55.7 + - - +
294G HIS* 4.7 2.4 + - - +
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Residues in contact with GLY 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ARG 3.7 1.0 - - - +
31G VAL* 3.9 0.7 - - - -
32G THR* 2.9 35.2 + - - +
118G VAL* 3.3 6.7 - - - +
119G LYS* 1.3 82.7 - - - +
121G LEU* 1.3 60.8 + - - +
293G TYR* 3.4 18.6 - - - -
294G HIS* 3.7 11.4 - - - -
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Residues in contact with LEU 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G PHE* 3.5 36.3 - - + -
30G ARG 3.6 1.3 - - - +
31G VAL* 3.8 20.6 - - + -
46G VAL* 4.4 16.4 - - + -
112G ILE* 3.6 56.1 - - + +
113G PHE* 3.2 22.2 - - + +
118G VAL* 4.5 12.3 - - + -
120G GLY* 1.3 74.1 - - - +
122G ARG* 1.3 59.9 + - - +
293G TYR 3.3 1.0 + - - -
294G HIS* 3.1 10.9 + - - +
295G GLY 2.9 20.3 + - - -
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Residues in contact with ARG 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G PHE* 3.3 5.5 - - - -
30G ARG* 2.8 50.7 + - + -
121G LEU* 1.3 72.8 - - - +
123G LEU* 1.3 72.5 + - - +
124G GLU* 3.0 36.6 + - - +
288G PHE 5.0 0.6 + - - -
289G THR 3.0 28.1 + - - -
290G ARG 4.9 0.8 + - - -
291G ASN 3.6 14.4 + - - +
292G PRO* 3.7 18.4 - - - +
293G TYR 3.8 3.1 - - - -
294G HIS 3.5 27.1 - - - +
295G GLY 3.4 4.5 - - - -
296G ILE 4.0 2.8 - - - -
297G SER* 3.5 29.7 + - - +
298G MET 4.7 0.6 - - - +
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Residues in contact with LEU 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G ALA* 4.2 7.0 - - + -
28G VAL 3.6 11.2 - - - +
29G PHE* 3.6 35.9 - - + -
105G LEU* 5.8 0.9 - - + -
108G ILE* 4.0 24.5 - - + +
109G ALA* 4.1 14.8 - - + -
113G PHE* 4.3 6.8 - - + -
121G LEU 4.2 0.6 + - - -
122G ARG* 1.3 68.5 - - - +
124G GLU* 1.3 59.4 + - - +
125G ASP 3.8 13.2 - - - +
126G LEU* 4.2 12.8 - - + -
295G GLY 2.9 15.2 + - - +
296G ILE* 4.4 9.9 - - + -
297G SER* 2.9 28.2 + - - -
300G VAL* 3.7 19.6 - - + +
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Residues in contact with GLU 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G VAL* 2.6 21.9 + - + +
29G PHE 4.5 0.2 - - - -
30G ARG* 3.7 27.0 + - + +
86G ILE* 4.7 0.7 - - + -
122G ARG* 3.0 44.8 + - - +
123G LEU* 1.3 74.1 - - - +
125G ASP* 1.3 60.9 + - - +
292G PRO 4.1 1.0 - - - +
297G SER* 3.7 7.6 + - - -
299G PHE* 3.7 14.7 - - - +
300G VAL* 3.8 1.9 - - - +
350G PHE* 3.3 55.0 - - + +
351G HIS* 3.7 16.1 + - - -
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Residues in contact with ASP 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G ILE 3.8 0.2 - - - +
27G ALA* 3.7 2.6 - - - -
28G VAL* 2.9 35.1 + - + -
123G LEU* 3.5 6.1 - - - +
124G GLU* 1.3 82.5 - - - +
126G LEU* 1.3 80.0 + - - +
127G TYR 4.2 1.1 - - - -
299G PHE* 3.5 22.9 - - + -
300G VAL* 3.7 10.3 - - - +
303G LYS* 3.2 21.0 + - - -
350G PHE 3.6 15.0 - - - +
351G HIS* 3.5 2.6 - - - -
352G LEU* 2.8 36.1 + - - +
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Residues in contact with LEU 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G ILE* 4.3 15.0 - - + -
26G ILE 3.5 11.4 - - - +
27G ALA* 4.0 20.0 - - + -
104G LEU* 4.6 1.8 - - + -
105G LEU* 4.6 9.4 - - + -
108G ILE* 3.5 37.2 - - + -
123G LEU* 4.2 9.6 - - + -
125G ASP* 1.3 81.3 + - - +
127G TYR* 1.3 57.1 + - - +
128G PHE* 3.7 21.6 + - + -
300G VAL* 4.1 25.4 - - + +
303G LYS* 2.5 39.0 + - + +
304G LEU* 4.8 5.8 - - + -
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Residues in contact with TYR 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G LYS* 2.6 42.3 + - + +
24G ASP 3.7 22.7 - - - -
25G ILE* 3.7 7.1 - - - +
26G ILE* 2.8 57.6 + - + +
125G ASP* 4.2 1.2 - - - -
126G LEU* 1.3 71.9 - - - +
128G PHE* 1.3 75.2 + - - +
129G PRO* 3.8 11.1 - - - +
130G GLU 5.1 0.5 + - - -
303G LYS* 4.0 1.3 - - - +
352G LEU* 4.1 17.9 - - + +
353G GLU 3.2 27.6 - - - -
354G GLN* 3.4 20.2 - - - +
355G LYS 5.3 1.3 - - - -
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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