Contacts of the strand formed by residues 199 - 205 (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 TYR 199 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194D PHE* 5.2 0.9 - - - -
197D GLY 4.5 8.3 - - - -
198D GLU* 1.3 78.9 - - - +
200D ALA* 1.3 59.8 + - - +
266D ASN* 3.9 25.8 - - + +
267D LYS 3.3 1.1 - - - -
268D ARG* 3.6 43.0 - - + -
313D PRO* 4.0 3.6 - - - +
314D ALA* 3.0 32.2 + - + +
317D PRO* 4.8 7.4 - - + -
318D ASN 6.1 0.2 - - - -
319D ASP* 3.9 42.2 + - + -
320D GLN 4.1 11.7 - - - -
321D PRO* 4.9 7.9 - - + +
322D ARG* 3.2 26.2 + - - -
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Residues in contact with ALA 200 (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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194D PHE* 3.8 20.0 - - + -
198D GLU 4.0 0.2 + - - -
199D TYR* 1.3 74.8 - - - +
201D ASP* 1.3 64.9 + - - +
202D VAL* 3.9 1.8 - - + -
266D ASN 3.7 0.2 - - - -
267D LYS* 2.6 49.5 + - - +
269D LEU* 4.1 20.2 - - + -
311D PHE* 4.6 9.2 - - + -
312D ARG 3.1 16.4 - - - +
314D ALA* 3.7 1.1 - - - +
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Residues in contact with ASP 201 (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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26D PHE* 3.7 5.8 - - - -
200D ALA* 1.3 71.9 - - - +
202D VAL* 1.3 59.9 + - - +
263D THR* 4.3 6.7 - - + -
264D GLU 3.6 7.0 - - - +
265D LEU* 3.3 13.6 - - - +
266D ASN* 3.0 25.1 + - - +
310D ARG 3.3 5.0 - - - +
311D PHE* 3.7 0.3 - - - -
312D ARG* 2.6 70.5 + - - +
314D ALA* 3.6 12.1 - - - +
315D VAL* 3.0 22.9 + - - +
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Residues in contact with VAL 202 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74D ILE* 5.2 0.2 - - + -
200D ALA* 3.9 2.0 + - + +
201D ASP* 1.3 73.1 - - - +
203D ALA* 1.3 68.4 + - - +
262D ARG 3.8 1.2 - - - +
263D THR* 4.4 0.9 - - - -
264D GLU* 2.9 35.6 + - + +
267D LYS* 3.9 28.5 - - + -
269D LEU* 5.9 0.2 - - + -
297D VAL* 4.7 8.3 - - + -
301D VAL* 3.5 33.7 - - + -
302D PRO* 4.0 5.8 - - + +
309D VAL* 4.2 9.0 - - + -
310D ARG 3.2 9.2 - - - +
311D PHE* 4.0 27.8 - - + -
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Residues in contact with ALA 203 (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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24D PRO* 3.8 18.6 - - + +
25D ARG 5.6 0.2 - - - +
26D PHE* 3.4 29.2 - - + -
201D ASP 3.9 1.4 + - - -
202D VAL* 1.3 76.1 - - - +
204D GLY* 1.3 59.9 + - - +
261D GLN* 5.1 3.8 - - + +
262D ARG 3.1 7.2 - - - +
263D THR* 3.6 16.4 - - - +
302D PRO* 4.3 3.1 - - - -
309D VAL* 3.6 8.5 - - - +
310D ARG* 3.0 27.8 + - + +
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Residues in contact with GLY 204 (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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24D PRO* 3.2 17.0 - - - +
203D ALA* 1.3 77.1 - - - +
205D VAL* 1.3 65.6 + - - -
206D THR 3.6 1.4 + - - -
261D GLN* 4.3 1.1 - - - +
262D ARG* 2.9 33.3 + - - +
302D PRO* 4.1 12.8 - - - +
307D ARG* 5.4 0.2 - - - -
308D LEU 4.5 6.3 - - - -
309D VAL* 4.9 4.5 - - - -
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Residues in contact with VAL 205 (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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19D SER* 3.8 10.8 - - - +
21D SER 3.5 17.7 - - - +
22D GLU* 3.2 24.9 + - - +
24D PRO* 4.1 5.7 - - + +
204D GLY* 1.3 72.5 - - - -
206D THR* 1.3 59.6 + - - +
259D TYR* 3.5 56.5 - - + +
260D HIS 3.2 4.5 - - - +
261D GLN* 4.4 8.5 - - + -
303D GLY* 3.2 4.1 - - - -
307D ARG* 2.6 43.0 + - - +
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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