Contacts of the strand formed by residues 292 - 298 (chain D) in PDB entry 1KD1
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 GLY 292 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75D GLU* 4.6 5.3 + - - -
274D GLU* 3.0 11.0 - - - -
275D GLY 2.8 28.0 + - - +
290D VAL* 4.3 2.0 - - - +
291D ASP* 1.3 78.5 - - - +
293D PRO* 1.3 77.1 - - - +
294D TYR* 3.3 8.0 + - - +
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Residues in contact with PRO 293 (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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75D GLU* 3.6 8.4 - - - +
76D THR* 3.1 37.5 + - - +
77D PRO* 3.7 24.5 - - + +
78D PRO* 4.2 11.9 - - + -
273D GLY 3.6 9.2 - - - +
274D GLU* 3.8 21.5 - - + +
292D GLY* 1.3 82.8 - - - +
294D TYR* 1.3 58.6 + - - +
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Residues in contact with TYR 294 (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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73D VAL* 4.7 4.0 - - + -
74D ILE 3.5 13.0 - - - +
75D GLU* 4.6 0.4 - - - -
76D THR* 3.3 7.9 + - - -
271D ASP* 3.7 14.6 + - - -
272D ILE* 3.5 5.5 - - - +
273D GLY* 3.0 46.2 + - - +
274D GLU 3.3 24.5 - - - -
275D GLY 4.0 3.1 - - - -
277D GLU* 3.7 17.8 + - - +
278D PRO* 3.2 43.9 - - + +
290D VAL* 4.5 12.8 - - + -
292D GLY 3.4 19.5 - - - +
293D PRO* 1.3 76.0 - - - +
295D THR* 1.3 67.7 + - - +
296D LEU* 3.8 25.9 - - + +
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Residues in contact with THR 295 (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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72D THR 3.6 1.4 - - - +
73D VAL* 3.9 1.6 - - - -
74D ILE* 2.8 31.9 + - - +
76D THR* 2.9 34.6 + - - +
190D MET* 3.3 18.7 - - - +
269D LEU* 4.1 18.2 - - + -
271D ASP 3.5 8.3 - - - +
272D ILE* 4.3 8.0 - - + +
294D TYR* 1.3 76.4 + - - +
296D LEU* 1.3 66.6 + - - +
297D VAL* 3.8 20.4 + - + -
311D PHE* 4.3 8.3 - - + -
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Residues in contact with LEU 296 (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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49D THR* 5.4 1.8 - - - +
51D VAL* 5.3 4.9 - - + -
71D VAL* 3.5 25.6 - - + -
73D VAL* 3.7 25.4 - - + -
269D LEU* 3.7 3.8 - - - -
270D ILE* 3.0 34.8 + - + +
271D ASP* 2.7 38.2 + - + +
278D PRO* 4.1 13.7 - - + -
294D TYR* 3.8 19.5 - - + +
295D THR* 1.3 76.7 - - - +
297D VAL* 1.3 62.1 + - - +
327D VAL* 5.9 1.3 - - + -
330D VAL* 4.8 23.1 - - + -
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Residues in contact with VAL 297 (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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71D VAL* 3.2 5.8 - - - +
72D THR 2.7 44.0 + - - +
74D ILE* 3.9 15.7 - - + -
202D VAL* 4.7 2.0 - - + -
267D LYS* 4.0 24.2 - - + -
268D ARG 3.9 4.7 - - - +
269D LEU* 4.2 5.6 - - + -
295D THR* 4.0 9.0 - - + -
296D LEU* 1.3 76.4 - - - +
298D LYS* 1.3 77.1 + - - +
299D GLY 3.5 0.9 - - - +
301D VAL* 4.0 22.2 - - + -
311D PHE* 3.7 29.4 - - + -
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Residues in contact with LYS 298 (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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2765A C 4.0 21.6 + - - +
2766A A 3.9 23.1 + - - +
69D VAL* 3.8 30.2 - - + +
70D PRO* 3.7 5.8 - - - -
267D LYS* 3.8 13.0 - - - +
268D ARG* 3.0 51.1 + - + +
270D ILE* 3.9 14.5 - - + +
296D LEU 3.9 0.8 + - - -
297D VAL* 1.3 82.3 - - - +
299D GLY* 1.3 65.8 + - - +
300D SER 3.7 1.4 + - - -
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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