Contacts of the strand formed by residues 238 - 244 (chain D) in PDB entry 7KHC
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 ILE 238 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D PRO* 5.7 2.9 - - - +
110D PRO* 3.9 25.6 - - + -
111D THR 3.4 15.3 - - - +
112D ALA* 3.7 25.6 - - + -
124D ILE* 4.9 7.4 - - + -
182D ALA* 4.4 6.1 - - + +
185D ILE* 4.2 19.7 - - + -
186D GLN* 4.3 24.0 - - + +
189D LEU* 3.9 23.3 - - + -
235D GLU* 2.9 22.2 + - - +
236D TRP* 3.0 7.6 - - - +
237D MET* 1.3 80.7 - - + +
239D LEU* 1.3 63.2 + - - +
240D THR* 3.8 5.0 + - - +
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Residues in contact with LEU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1334C GLY* 4.9 14.1 - - - +
30D ILE* 6.1 4.5 - - + -
107D LEU* 4.3 6.4 - - + +
110D PRO* 3.5 5.4 - - - +
111D THR* 2.6 44.7 + - + +
113D HIS* 3.7 46.0 - - + +
116D PHE* 6.0 0.7 - - + -
236D TRP 3.7 17.3 - - - +
238D ILE* 1.3 73.2 - - - +
240D THR* 1.3 61.3 + - - +
241D VAL 4.6 9.4 - - - +
242D LEU* 3.9 28.3 - - + -
243D PRO* 6.4 0.2 - - + -
303D VAL* 5.0 6.5 - - + -
307D LEU* 4.4 9.0 - - + -
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Residues in contact with THR 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PRO* 4.6 20.1 - - + +
30D ILE* 6.2 0.4 - - - +
31D ARG* 4.5 10.8 - - - +
106D GLU* 5.0 2.7 - - - +
107D LEU* 3.0 41.0 + - - +
110D PRO* 5.0 16.1 - - + +
186D GLN* 5.5 4.9 + - - -
238D ILE* 3.8 5.5 + - - +
239D LEU* 1.3 76.0 + - - +
241D VAL* 1.3 72.5 + - + +
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Residues in contact with VAL 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PRO* 4.7 9.4 - - + +
30D ILE* 3.6 37.3 - - + +
31D ARG* 3.4 41.3 - - + +
104D HIS* 3.4 34.1 - - + -
105D ILE 3.2 17.7 - - - +
106D GLU* 3.4 11.7 - - - +
107D LEU 4.6 0.2 - - - +
239D LEU* 4.6 6.8 - - - +
240D THR* 1.3 85.6 + - + +
242D LEU* 1.3 60.3 + - - +
243D PRO* 3.9 0.6 - - - +
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Residues in contact with LEU 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332C SER 5.3 3.6 - - - +
1333C LEU 6.3 0.2 - - - -
1334C GLY 6.2 1.6 - - - +
104D HIS* 4.3 1.3 - - - -
105D ILE* 2.9 56.1 + - + +
107D LEU* 5.1 11.4 - - + +
239D LEU* 3.9 28.9 - - + -
240D THR 4.2 0.6 + - - -
241D VAL* 1.3 74.2 - - - +
243D PRO* 1.3 80.6 - - + +
244D VAL 3.8 0.2 + - - -
269D TYR* 5.0 4.9 - - + -
272D VAL* 5.0 10.5 - - + -
303D VAL* 5.2 11.2 - - + -
306D LEU* 4.2 29.2 - - + -
307D LEU* 4.6 14.4 - - + -
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Residues in contact with PRO 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1331C ARG 3.8 12.6 - - - +
1332C SER 3.2 29.3 - - - +
1333C LEU 4.0 6.3 - - - +
1334C GLY* 5.5 1.8 - - - -
30D ILE* 3.8 31.4 - - + +
33D TRP* 5.3 4.5 - - + -
34D SER* 6.0 0.2 - - - -
102D MET* 3.8 18.2 - - + -
103D GLY 3.2 13.9 - - - +
104D HIS* 4.0 2.7 - - + -
241D VAL 3.9 2.9 - - - +
242D LEU* 1.3 103.2 - - + +
244D VAL* 1.3 59.5 + - - +
269D TYR* 4.1 6.1 + - - -
306D LEU* 6.1 0.2 - - - +
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Residues in contact with VAL 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D VAL* 4.9 14.4 - - + -
56D LEU* 4.1 9.4 - - + -
62D PHE* 4.1 13.7 - - + -
102D MET* 3.8 7.8 - - - +
103D GLY* 2.9 48.0 + - - +
104D HIS* 3.6 5.8 - - - +
105D ILE* 5.5 2.2 - - + +
242D LEU 5.0 0.7 - - - +
243D PRO* 1.3 75.1 - - - +
245D LEU* 1.3 64.0 + - - +
246D PRO 3.6 0.5 - - - -
250D ARG* 3.7 14.1 - - - +
269D TYR* 3.2 39.5 - - + -
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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