Contacts of the strand formed by residues 255 - 264 (chain D) in PDB entry 1QD6
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 ASN 255 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ASP* 3.2 14.6 - - - +
243D SER* 5.0 1.2 + - - -
244D GLY* 3.2 27.2 + - - -
245D TYR* 3.5 34.9 + - + +
254D PHE* 1.3 82.1 - - - +
256D GLN* 1.3 71.0 + - - +
257D THR* 5.4 0.3 + - - -
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Residues in contact with GLN 256 (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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45D THR* 2.8 26.7 + - - +
46D SER* 3.5 5.6 - - - -
47D ASP* 3.5 19.2 - - - +
48D LEU* 5.3 1.7 - - - +
49D ASN 5.5 0.3 + - - -
110D ARG* 5.2 0.7 + - - -
242D TYR* 4.0 2.9 - - + +
243D SER* 3.5 2.3 - - - -
244D GLY 3.0 29.3 + - - +
247D GLU* 3.7 27.1 + - + +
251D ASP* 2.9 42.0 + - - +
254D PHE* 3.7 12.5 + - + -
255D ASN* 1.3 79.4 + - - +
257D THR* 1.3 63.4 + - - +
258D ARG* 3.5 15.3 + - + +
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Residues in contact with THR 257 (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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44D GLN 4.0 0.5 - - - +
45D THR* 3.4 2.2 - - - -
46D SER* 2.8 44.3 + - - -
241D VAL* 4.5 13.7 - - + -
242D TYR 3.2 8.7 - - - +
243D SER* 2.8 23.9 + - - +
255D ASN* 5.4 0.3 + - - -
256D GLN* 1.3 73.2 - - - +
258D ARG* 1.3 64.9 - - - +
259D VAL* 4.4 2.6 + - + -
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Residues in contact with ARG 258 (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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43D THR* 2.8 31.8 + - + -
44D GLN 3.4 10.5 - - - +
45D THR* 3.7 17.7 - - - +
48D LEU* 5.3 0.2 - - - +
64D LYS 3.8 13.3 + - - -
66D GLU* 2.5 46.3 + - - +
68D LYS* 4.6 2.7 - - - +
97D TRP* 3.8 9.2 - - - +
110D ARG* 3.6 9.5 - - - +
240D GLN* 3.8 4.2 + - - +
241D VAL* 3.2 5.4 - - - +
242D TYR* 2.7 50.3 + - + +
247D GLU* 3.2 38.3 + - - +
256D GLN* 3.5 20.4 + - + -
257D THR* 1.3 77.9 - - - +
259D VAL* 1.3 63.8 - - - +
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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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43D THR* 3.1 5.0 - - - -
44D GLN* 2.9 43.2 + - + +
239D THR* 5.1 6.1 - - + -
240D GLN 3.4 9.0 - - - +
241D VAL* 4.3 16.2 - - + -
257D THR* 5.9 2.2 - - + +
258D ARG* 1.3 75.7 - - - +
260D GLY* 1.3 65.3 + - - +
261D VAL* 5.5 3.4 - - + -
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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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41D ILE* 4.2 8.7 - - - -
42D TYR 3.1 12.3 - - - -
43D THR* 3.8 12.3 - - - +
239D THR* 3.3 4.9 - - - +
240D GLN* 2.8 41.8 + - - +
259D VAL* 1.3 77.8 - - - +
261D VAL* 1.3 66.4 + - - +
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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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41D ILE* 3.7 5.5 - - - +
42D TYR* 2.8 32.2 + - - +
237D LEU* 5.6 7.6 - - + -
238D TYR 3.4 9.0 - - - +
239D THR* 3.6 22.4 - - + +
259D VAL* 5.5 4.0 - - + -
260D GLY* 1.3 79.7 - - - +
262D GLY* 1.3 65.2 + - - +
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Residues in contact with GLY 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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40D LEU 3.4 10.5 - - - -
41D ILE* 3.6 3.7 - - - +
237D LEU* 3.7 11.4 - - - +
238D TYR 2.8 30.4 + - - -
261D VAL* 1.3 79.8 - - - +
263D VAL* 1.3 67.6 + - - +
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Residues in contact with VAL 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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270C HDS 3.5 28.0 - - + -
39D TYR* 3.3 5.5 - - - +
40D LEU* 2.8 47.8 + - + +
41D ILE* 4.4 0.4 - - - +
231D ILE* 4.5 9.4 - - + -
235D VAL* 4.2 14.8 - - + -
236D ARG 3.2 11.2 - - - +
237D LEU* 5.1 3.8 - - + -
238D TYR* 4.3 2.9 - - - +
262D GLY* 1.3 79.1 - - - +
264D MET* 1.3 61.8 + - - +
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Residues in contact with MET 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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270C HDS 4.2 3.4 - - - -
37D THR* 3.9 28.7 - - + +
38D ASN 3.4 8.7 - - - +
39D TYR* 4.1 5.2 - - + +
228D SER* 3.8 12.3 - - - -
235D VAL* 3.6 4.3 - - - +
236D ARG* 2.7 38.4 + - + +
238D TYR* 3.7 47.8 - - + +
263D VAL* 1.3 78.7 - - - +
265D LEU* 1.3 65.4 + - - +
266D ASN 3.3 14.4 - - - +
267D ASP* 3.5 35.9 - - - +
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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