Contacts of the strand formed by residues 118 - 127 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A ARG* 3.1 31.0 + - - +
31H VAL* 4.3 10.3 - - + -
32H THR 3.1 15.0 - - - +
33H PRO* 4.4 1.6 - - + -
34H ALA* 3.9 0.7 - - - +
42H ALA* 5.5 3.4 - - + -
46H VAL* 5.5 2.5 - - + -
112H ILE 4.1 9.6 - - - +
113H PHE 4.9 0.4 - - - +
115H MET* 2.9 37.5 - - + +
116H LYS 2.8 3.9 + - - +
117H ARG* 1.3 81.8 - - - +
119H LYS* 1.3 58.9 + - - +
120H GLY 2.8 34.5 - - - +
121H LEU* 4.1 12.8 - - + +
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Residues in contact with LYS 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A ARG* 5.0 8.3 + - - +
32H THR* 2.6 37.7 + - + +
33H PRO 3.6 10.1 - - - +
34H ALA* 3.6 11.2 - - + +
35H GLU* 5.9 1.7 + - - +
118H VAL* 1.3 73.4 - - - +
120H GLY* 1.3 53.3 + - - -
294H HIS* 5.0 1.2 + - - -
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Residues in contact with GLY 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A ARG* 5.5 0.4 - - - -
30H ARG 3.8 0.6 - - - +
31H VAL* 3.9 0.3 - - - -
32H THR* 2.9 27.2 + - - -
118H VAL* 2.8 18.3 - - - +
119H LYS* 1.3 80.8 - - - +
121H LEU* 1.3 61.3 + - - -
293H TYR* 3.4 16.4 - - - -
294H HIS* 3.8 11.9 - - - -
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Residues in contact with LEU 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H PHE* 3.5 28.0 - - + -
30H ARG 3.7 2.7 - - - +
31H VAL* 3.5 32.8 - - + -
46H VAL* 4.1 18.4 - - + -
112H ILE* 3.6 51.8 - - + +
113H PHE* 3.0 29.5 - - + +
115H MET* 5.0 0.7 - - + -
118H VAL* 4.2 10.3 - - + -
120H GLY* 1.3 75.2 - - - +
122H ARG* 1.3 58.5 + - - +
293H TYR 3.2 3.2 + - - -
294H HIS* 3.2 10.5 + - + +
295H GLY 3.1 10.4 + - - -
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Residues in contact with ARG 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H PHE* 3.4 4.7 - - - -
30H ARG* 2.9 37.9 + - + -
121H LEU* 1.3 74.4 - - - +
123H LEU* 1.3 64.0 + - - +
124H GLU* 3.1 42.9 + - - +
289H THR* 3.2 28.5 + - - +
290H ARG 4.3 1.0 + - - -
291H ASN 3.3 26.1 + - - -
292H PRO* 3.7 20.7 - - - +
293H TYR 3.8 4.4 + - - -
294H HIS* 3.6 18.2 - - - +
295H GLY 3.3 7.4 - - - +
296H ILE 4.6 0.4 + - - -
297H SER* 3.4 34.3 + - - +
298H MET 5.1 0.6 - - - +
329H ILE* 5.8 7.5 - - - +
333H PHE* 6.3 0.8 - - - -
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Residues in contact with LEU 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ALA* 3.9 10.5 - - + -
28H VAL 3.7 7.0 - - - +
29H PHE* 3.6 36.0 - - + -
105H LEU* 5.9 2.7 - - + -
108H ILE* 3.9 20.0 - - + +
109H ALA* 4.1 14.1 - - + -
113H PHE* 4.3 8.1 - - + -
121H LEU 4.2 0.8 - - - -
122H ARG* 1.3 68.8 - - - +
124H GLU* 1.3 60.8 + - - +
125H ASP 3.7 22.0 - - - +
126H LEU* 5.0 7.6 - - + -
295H GLY 3.0 13.1 + - - +
296H ILE* 4.4 16.4 - - + -
297H SER* 3.1 24.6 + - - -
300H VAL* 3.9 17.5 - - + +
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Residues in contact with GLU 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H VAL* 2.6 22.7 + - + +
29H PHE 4.5 0.9 - - - -
30H ARG* 3.4 32.4 + - + +
86H ILE* 4.9 1.3 - - + -
122H ARG* 3.1 50.4 + - - +
123H LEU* 1.3 74.5 - - - +
125H ASP* 1.3 59.9 + - - +
292H PRO* 3.7 2.1 - - - +
297H SER* 3.9 6.4 + - - -
299H PHE* 3.9 14.9 - - - +
300H VAL* 3.9 1.8 - - - +
350H PHE* 3.9 44.0 - - + +
351H HIS* 3.8 14.6 + - - -
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Residues in contact with ASP 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H ILE 4.3 0.9 - - - -
27H ALA* 3.6 3.5 - - - -
28H VAL* 3.0 33.6 + - + -
123H LEU* 3.5 7.2 - - - +
124H GLU* 1.3 80.5 - - - +
126H LEU* 1.3 96.2 + - - +
127H TYR 4.7 0.9 - - - -
299H PHE* 3.4 26.1 - - + -
300H VAL* 3.8 10.5 - - - +
303H LYS* 3.3 12.3 + - - +
350H PHE 3.6 16.2 - - - +
351H HIS* 3.4 1.9 - - - -
352H LEU* 3.0 32.9 + - - +
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Residues in contact with LEU 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H ILE* 3.9 6.5 - - + -
26H ILE 3.4 11.7 - - - +
27H ALA* 4.0 4.3 - - + -
104H LEU* 4.1 14.8 - - + -
105H LEU* 4.7 13.7 - - + -
108H ILE* 3.6 39.3 - - + -
123H LEU* 5.0 7.4 - - + -
125H ASP* 1.3 90.0 + - - +
127H TYR* 1.3 56.0 + - - +
128H PHE* 3.8 28.4 + - + -
300H VAL* 4.2 19.1 - - + +
303H LYS* 2.6 35.5 + - + +
304H LEU* 4.7 9.6 - - + -
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Residues in contact with TYR 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H LYS* 2.8 43.9 + - + +
22H LYS* 5.6 0.7 - - - -
24H ASP 3.6 20.9 - - - -
25H ILE* 3.4 9.4 - - - +
26H ILE* 2.8 53.8 + - + +
125H ASP* 4.1 1.2 + - - +
126H LEU* 1.3 71.3 - - - +
128H PHE* 1.3 83.2 + - - +
129H PRO* 4.2 1.4 - - - +
130H GLU 5.0 1.2 + - - -
303H LYS* 3.9 1.6 - - - +
352H LEU* 4.0 17.0 - - + -
353H GLU 3.2 28.0 - - - -
354H GLN* 3.4 25.1 - - - +
355H LYS 5.2 1.1 - - - -
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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