Contacts of the strand formed by residues 258 - 266 (chain D) in PDB entry 6DKS
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 PHE 258 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111D GLU 4.4 0.2 - - - +
112D ALA* 5.2 0.7 - - - -
113D LEU* 5.7 0.4 + - - +
155D TYR* 3.3 35.5 + - + -
158D TRP* 3.4 44.2 - + + -
159D PRO* 5.2 0.8 - - - +
168D ALA* 3.5 23.3 - - + -
256D LYS 3.8 1.0 + - - -
257D PRO* 1.3 72.0 - - - +
259D VAL* 1.3 65.6 + - - +
260D GLY 3.4 0.9 + - - -
328D GLU* 3.5 25.1 - - + -
329D ILE 4.9 0.7 - - - -
330D MET* 3.6 30.6 - - + +
331D PRO* 4.2 10.8 - - + -
336D MET* 4.3 3.6 - - + -
339D PHE* 3.8 21.1 - + - -
340D TRP* 3.6 22.7 - + + -
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Residues in contact with VAL 259 (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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64D HIS* 3.4 5.5 - - - -
110D VAL* 3.6 30.3 - - + -
111D GLU 3.8 8.5 - - - +
112D ALA* 4.7 3.4 - - + -
257D PRO 3.9 4.9 - - - +
258D PHE* 1.3 69.2 - - - +
260D GLY* 1.3 61.4 + - - +
261D VAL* 5.5 0.7 - - + -
324D ALA* 3.4 45.1 - - + +
328D GLU* 2.9 27.2 + - - +
329D ILE* 3.6 19.3 - - + +
330D MET* 3.1 25.7 + - - +
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Residues in contact with GLY 260 (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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63D ALA* 4.5 8.3 - - - -
64D HIS* 3.8 5.6 - - - -
110D VAL* 3.5 4.0 - - - +
111D GLU* 2.8 51.6 + - - +
155D TYR* 4.5 3.8 + - - -
258D PHE 3.4 4.0 + - - -
259D VAL* 1.3 73.6 - - - +
261D VAL* 1.3 63.1 + - - +
330D MET* 4.4 8.5 - - - -
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Residues in contact with VAL 261 (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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63D ALA* 4.0 1.5 - - - +
64D HIS* 2.8 38.8 + - + +
92D PHE* 5.4 4.3 - - + +
93D THR* 4.4 16.2 - - + +
96D ALA* 3.8 20.4 - - + -
97D VAL* 5.1 0.2 - - + -
107D PRO* 3.9 28.5 - - + -
108D ILE 4.7 0.2 - - - +
109D ALA 3.3 12.1 - - - +
110D VAL* 4.3 19.1 - - + -
259D VAL* 5.5 0.7 - - + -
260D GLY* 1.3 74.9 - - - +
262D LEU* 1.4 59.8 + - - +
263D SER* 2.7 26.5 + - - +
329D ILE* 4.5 9.4 - - + -
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Residues in contact with LEU 262 (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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11D ILE* 4.9 6.3 - - + -
15D LYS* 4.2 31.0 - - + -
61D PHE* 4.3 23.6 - - + -
62D TRP* 3.8 28.5 - - - +
63D ALA* 4.2 3.6 - - - +
108D ILE* 2.8 45.4 + - + +
109D ALA* 2.8 17.1 + - + +
111D GLU* 3.9 17.9 + - - +
260D GLY 4.0 1.8 - - - -
261D VAL* 1.4 69.5 - - - +
263D SER* 1.3 53.4 + - - +
299D LEU* 3.7 30.7 - - + -
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Residues in contact with SER 263 (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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60D ILE 3.3 1.7 - - - +
61D PHE* 3.3 6.4 - - - +
62D TRP 2.8 35.3 + - - +
64D HIS* 3.7 7.7 - - - +
67D PHE* 3.4 9.1 - - - -
97D VAL* 3.4 26.7 - - - +
105D ALA* 3.8 9.2 - - - -
106D TYR 3.3 12.1 - - - -
107D PRO* 4.4 0.2 - - - +
108D ILE* 3.8 3.1 - - - -
261D VAL* 2.7 23.6 + - - +
262D LEU* 1.3 74.2 + - - +
264D ALA* 1.3 61.2 + - - +
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Residues in contact with ALA 264 (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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59D ILE* 4.0 7.4 - - + -
60D ILE 3.2 4.7 - - - -
61D PHE* 3.7 22.4 - - + -
105D ALA* 3.4 3.8 - - - -
106D TYR* 2.8 44.0 + - + +
108D ILE* 3.5 17.7 - - + +
263D SER* 1.3 71.7 - - - +
265D GLY* 1.3 59.7 + - - +
280D LEU* 3.7 18.9 - - + +
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Residues in contact with GLY 265 (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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59D ILE* 3.2 5.4 - - - +
60D ILE* 2.8 38.8 + - - +
67D PHE* 3.4 20.2 - - - -
76D LEU* 4.1 3.4 - - - -
79D ILE* 5.3 0.2 - - - -
104D ILE 3.9 6.5 - - - -
105D ALA* 3.8 8.5 - - - -
264D ALA* 1.3 74.8 - - - +
266D ILE* 1.3 63.3 + - - -
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Residues in contact with ILE 266 (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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58D ASP 3.3 10.5 - - - +
59D ILE* 4.6 0.9 - - + -
76D LEU* 3.4 7.1 - - - +
77D ALA* 2.8 40.8 + - + -
79D ILE* 3.7 24.7 - - + +
104D ILE 4.5 3.2 + - - -
106D TYR* 3.9 15.7 - - + +
265D GLY* 1.3 75.9 - - - +
267D ASN* 1.3 69.1 + - - +
270D SER* 4.8 3.1 - - - +
273D LYS* 3.7 27.1 - - + +
276D ALA* 3.9 31.0 - - + -
277D LYS* 4.2 10.3 - - + +
280D LEU* 4.0 12.6 - - + -
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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