Contacts of the helix formed by residues 300 - 313 (chain D) in PDB entry 3Q2K
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 300 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D ASN* 4.5 0.2 - - - +
131D GLN* 3.5 35.1 - - - +
134D ARG* 5.2 0.3 - - - +
135D ASN* 6.1 0.7 - - - -
296D VAL* 3.7 16.6 + - - -
298D GLY 4.3 0.6 - - - -
299D PHE* 1.3 71.9 - - - +
301D HIS* 1.3 69.2 + - - +
302D PRO* 3.5 3.2 - - - -
303D LEU* 3.8 14.5 + - - +
304D TYR 3.8 4.3 + - - -
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Residues in contact with HIS 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ILE* 4.5 6.5 - - + +
24D ASN* 3.7 37.6 + - + +
25D HIS* 3.5 29.7 + + - -
28D ALA* 3.8 7.2 - - + -
102D GLU* 2.8 21.7 + - - -
129D VAL* 3.8 13.5 - - + +
131D GLN* 2.9 35.0 + - - -
300D GLY* 1.3 79.0 + - - +
302D PRO* 1.3 74.1 - - + +
304D TYR* 2.7 18.8 + + - +
305D TYR* 3.0 18.1 + + + -
500D NAI 3.6 10.6 + - - -
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Residues in contact with PRO 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ASN 4.8 1.3 - - - +
27D GLY 5.6 0.7 - - - -
28D ALA* 4.0 24.5 - - + +
31D GLN* 3.8 39.5 - - + +
32D HIS* 3.1 14.1 + - - +
296D VAL* 5.8 4.3 - - + -
299D PHE* 3.9 20.9 - - + +
300D GLY 3.5 4.0 - - - -
301D HIS* 1.3 93.7 - - + +
303D LEU* 1.3 64.1 + - - +
305D TYR* 3.2 2.0 + - + +
306D ASP 3.1 16.3 + - - -
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Residues in contact with LEU 303 (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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134D ARG* 4.0 50.4 + - + +
135D ASN* 6.3 0.4 - - - -
292D GLU 5.8 1.8 - - - +
296D VAL* 5.0 22.2 - - + -
300D GLY* 3.8 11.6 + - - +
301D HIS 3.2 0.2 - - - -
302D PRO* 1.3 80.2 - - - +
304D TYR* 1.3 61.3 + - - +
306D ASP* 3.1 26.8 - - + +
307D ASN* 3.5 3.6 + - - +
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Residues in contact with TYR 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D VAL* 4.1 6.5 - - + +
127D PHE* 3.3 21.0 - + - +
128D VAL 2.8 34.3 + - - -
129D VAL* 3.6 26.5 - - + -
130D LYS 3.7 23.3 - - - -
131D GLN* 4.4 11.2 - - + -
134D ARG* 4.5 14.6 - - + +
300D GLY 3.8 8.0 + - - +
301D HIS* 2.7 14.5 + + - +
303D LEU* 1.3 76.1 - - - +
305D TYR* 1.3 70.7 + + - +
307D ASN* 3.2 15.5 + - + +
308D VAL* 3.1 43.6 + - + +
320D THR* 3.8 16.1 + - - -
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Residues in contact with TYR 305 (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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13D PHE* 3.9 37.9 - + - -
25D HIS* 2.6 42.5 + + - +
28D ALA* 3.7 25.8 - - + +
29D ILE* 4.1 18.8 - - + +
32D HIS* 4.1 13.7 - - + +
77D VAL* 3.1 22.0 - - + +
100D VAL* 4.7 9.8 - - + +
301D HIS* 3.0 23.3 + + + -
302D PRO 3.5 8.7 - - - +
304D TYR* 1.3 85.4 - + - +
306D ASP* 1.3 60.5 + - - +
308D VAL* 3.7 8.0 - - + +
309D ILE* 2.7 38.2 + - + +
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Residues in contact with ASP 306 (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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32D HIS* 3.4 17.2 + - + -
35D ARG* 2.3 31.3 + - - +
134D ARG* 5.3 5.5 + - - +
302D PRO 3.1 7.8 + - - +
303D LEU* 3.1 23.2 - - + +
305D TYR* 1.3 77.7 - - - +
307D ASN* 1.3 57.0 + - - +
309D ILE* 3.6 1.6 - - - +
310D ASN* 2.9 48.3 + - - -
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Residues in contact with ASN 307 (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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127D PHE* 4.9 2.1 - - - -
134D ARG* 4.6 12.5 - - - +
303D LEU 3.5 4.8 + - - +
304D TYR* 3.2 18.4 + - + +
306D ASP* 1.3 79.0 - - - +
308D VAL* 1.3 66.2 + - - +
310D ASN* 4.1 7.0 - - - +
311D CYS* 3.2 19.4 + - - +
316D CYS* 4.2 11.5 - - - +
317D GLU 3.0 22.6 + - - -
318D PRO* 4.2 2.6 - - - +
319D GLU* 3.3 45.8 + - - +
320D THR 4.4 2.6 + - - -
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Residues in contact with VAL 308 (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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13D PHE* 4.1 15.7 - - + -
100D VAL* 4.4 8.7 - - + -
127D PHE* 3.6 42.3 - - + -
304D TYR* 3.1 42.0 + - + +
305D TYR* 3.2 13.4 + - + +
307D ASN* 1.3 77.0 - - - +
309D ILE* 1.3 64.6 + - - +
311D CYS* 3.2 3.6 + - - +
312D LEU* 3.0 37.6 + - + +
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Residues in contact with ILE 309 (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* 5.1 4.9 - - + +
13D PHE* 4.3 22.4 - - + -
29D ILE* 5.6 1.8 - - + -
32D HIS* 3.4 39.9 - - + +
35D ARG* 3.1 39.9 - - + +
36D ALA* 4.3 15.3 - - + -
305D TYR* 2.7 26.0 + - + +
306D ASP 3.6 2.5 - - - +
308D VAL* 1.3 74.1 - - - +
310D ASN* 1.3 62.8 + - - +
311D CYS 3.0 0.7 + - - -
312D LEU* 3.1 15.5 + - - +
313D ARG* 3.2 29.2 + - - +
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Residues in contact with ASN 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ARG* 2.7 30.1 + - - -
306D ASP* 2.9 40.6 + - - +
307D ASN* 4.1 4.8 - - - +
309D ILE* 1.3 75.8 - - - +
311D CYS* 1.3 59.8 + - - +
313D ARG* 3.3 11.0 + - - +
315D ASP* 3.0 38.5 + - + +
316D CYS* 3.7 28.3 - - + -
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Residues in contact with CYS 311 (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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125D ARG* 2.8 45.5 + - - -
127D PHE* 3.7 22.2 - - + -
307D ASN 3.2 15.5 + - - +
308D VAL 3.2 4.5 + - - +
309D ILE 3.1 0.6 - - - -
310D ASN* 1.3 79.4 - - - +
312D LEU* 1.3 63.0 + - - +
314D GLY* 3.2 13.3 + - - -
316D CYS* 3.8 19.9 - - + +
317D GLU 4.3 8.1 - - - +
318D PRO* 3.7 16.4 - - - -
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Residues in contact with LEU 312 (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* 4.0 44.6 - - + +
13D PHE* 4.4 3.4 - - + -
74D ASP* 5.5 1.1 - - + -
75D ALA* 4.2 17.9 - - + -
98D HIS* 3.6 37.5 - - + +
125D ARG* 4.6 7.0 - - + +
127D PHE* 4.0 19.7 - - + -
308D VAL* 3.0 33.4 + - + +
309D ILE* 3.8 4.3 - - - +
311D CYS* 1.3 77.4 - - - +
313D ARG* 1.3 57.9 + - - +
314D GLY 3.2 3.4 + - - -
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Residues in contact with ARG 313 (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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9D ARG 5.8 4.3 - - - +
11D ILE* 4.7 14.8 - - + -
35D ARG* 3.0 58.5 + - - +
309D ILE* 3.2 22.9 + - - +
310D ASN* 3.6 8.9 - - - +
311D CYS 3.1 1.0 - - - -
312D LEU* 1.3 77.4 - - - +
314D GLY* 1.3 55.1 + - - +
315D ASP* 3.0 25.4 + - - +
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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