Contacts of the helix formed by residues 300 - 313 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291D TYR* 4.2 0.2 + - - -
131M GLN* 3.5 34.0 - - - +
134M ARG* 5.5 0.2 - - - +
135M ASN* 6.1 1.1 - - - -
296M VAL* 3.8 6.5 + - - -
298M GLY 3.6 3.6 + - - -
299M PHE* 1.3 76.6 - - - +
301M HIS* 1.3 67.1 + - - +
302M PRO* 3.4 0.4 - - - -
303M LEU* 3.3 18.6 + - - +
304M TYR 3.4 8.3 + - - -
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Residues in contact with HIS 301 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D ARG* 4.7 1.6 - - - -
291D TYR* 3.9 0.6 + - - +
21M ILE* 3.6 25.1 - - + -
24M ASN* 3.6 24.5 + - + +
25M HIS* 3.4 28.5 + + - -
28M ALA* 3.7 16.6 - - + -
102M GLU* 3.1 21.0 + - - -
129M VAL* 4.2 12.3 - - + -
131M GLN* 3.5 22.5 + - - -
300M GLY* 1.3 77.9 + - - +
302M PRO* 1.3 73.0 - - + +
304M TYR* 3.1 8.9 + - + +
305M TYR* 2.8 30.6 + + + -
500M NAI 3.7 8.3 + - - -
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Residues in contact with PRO 302 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D TYR* 2.6 45.1 - - + +
28M ALA* 4.1 11.2 - - + -
31M GLN* 3.7 33.9 - - + +
32M HIS* 2.8 30.1 + - - +
296M VAL* 6.3 0.9 - - + -
299M PHE* 3.4 15.5 - - + +
301M HIS* 1.3 82.5 - - + +
303M LEU* 1.3 58.8 + - + +
305M TYR 3.4 0.2 + - - -
306M ASP 3.0 14.4 + - - -
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Residues in contact with LEU 303 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134M ARG* 4.1 42.2 - - + +
292M GLU* 4.4 17.0 - - - +
296M VAL* 4.7 26.7 - - + -
299M PHE 5.5 1.8 - - - +
300M GLY* 3.3 9.7 + - - +
301M HIS 3.1 0.4 - - - -
302M PRO* 1.3 79.0 - - + +
304M TYR* 1.3 66.8 + - - +
306M ASP* 3.2 25.0 + - + +
307M ASN 3.4 4.0 + - - -
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Residues in contact with TYR 304 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100M VAL* 4.6 6.5 - - + -
127M PHE* 3.4 19.8 - + - +
128M VAL 2.9 33.2 + - - -
129M VAL* 3.7 24.7 - - + -
130M LYS 3.8 22.2 - - - -
131M GLN* 4.0 21.5 - - + -
134M ARG* 4.3 14.3 - - + +
300M GLY 3.4 3.8 + - - +
301M HIS* 3.1 11.2 + + - +
303M LEU* 1.3 78.5 - - - +
305M TYR* 1.3 72.5 + + - +
307M ASN* 3.2 16.2 + - + +
308M VAL* 3.1 40.4 + - + +
319M GLU* 5.7 3.1 - - + -
320M THR* 3.6 15.0 + - - -
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Residues in contact with TYR 305 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M PHE* 3.9 36.8 - + - -
25M HIS* 2.6 41.9 + + - +
28M ALA* 3.4 28.3 - - + -
29M ILE* 4.0 18.4 - - + +
32M HIS* 4.2 14.1 - - + -
77M VAL* 3.2 23.8 - - + +
100M VAL* 4.3 6.6 - - + +
301M HIS* 2.8 26.4 + + + +
302M PRO 3.8 3.8 - - - +
304M TYR* 1.3 78.6 - + - +
306M ASP* 1.3 57.7 + - - +
308M VAL* 3.4 13.6 - - + +
309M ILE* 2.7 42.3 + - + +
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Residues in contact with ASP 306 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M HIS* 3.6 22.6 + - + -
35M ARG* 3.5 20.9 + - - +
302M PRO 3.0 9.0 + - - +
303M LEU* 3.2 20.6 - - + +
305M TYR* 1.3 78.2 - - - +
307M ASN* 1.3 64.5 + - - +
309M ILE* 3.3 1.0 + - - +
310M ASN* 3.1 45.3 + - - +
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Residues in contact with ASN 307 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127M PHE* 4.6 5.5 - - - -
134M ARG* 5.2 0.7 - - - -
303M LEU 3.4 4.6 + - - +
304M TYR* 3.2 16.2 + - + +
306M ASP* 1.3 82.5 + - - +
308M VAL* 1.3 67.6 + - - +
310M ASN* 4.0 7.7 - - - +
311M CYS* 3.1 19.6 + - - +
316M CYS* 3.8 11.7 - - - -
317M GLU 3.4 22.2 + - - -
318M PRO* 4.1 4.0 - - - +
319M GLU* 3.3 54.4 + - + +
320M THR 4.7 1.0 + - - -
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Residues in contact with VAL 308 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M PHE* 4.1 15.5 - - + -
100M VAL* 4.1 16.6 - - + -
127M PHE* 3.8 29.6 - - + -
304M TYR* 3.1 48.3 + - + +
305M TYR* 3.0 17.5 + - + +
307M ASN* 1.3 78.5 - - - +
309M ILE* 1.3 64.8 + - - +
311M CYS* 3.6 2.3 - - - +
312M LEU* 3.2 37.1 + - + +
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Residues in contact with ILE 309 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M ILE* 4.6 9.4 - - + +
13M PHE* 4.3 21.1 - - + -
29M ILE* 6.0 0.9 - - - -
32M HIS* 3.4 44.6 - - + +
35M ARG* 3.5 35.7 - - + +
36M ALA* 4.1 13.2 - - + -
305M TYR* 2.7 28.0 + - + +
306M ASP 3.9 3.1 - - - +
308M VAL* 1.3 73.5 - - - +
310M ASN* 1.3 61.8 + - - +
312M LEU* 3.1 8.9 + - - +
313M ARG* 3.1 34.2 + - + +
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Residues in contact with ASN 310 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M ARG* 2.6 34.2 + - - +
306M ASP* 3.1 35.2 + - - +
307M ASN* 4.0 4.1 - - - +
309M ILE* 1.3 75.0 - - - +
311M CYS* 1.3 53.8 - - - +
313M ARG* 3.4 4.2 + - - +
314M GLY 3.4 3.3 + - - -
315M ASP* 2.5 62.2 + - + +
316M CYS* 3.7 12.2 - - - -
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Residues in contact with CYS 311 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125M ARG* 3.7 35.9 + - - -
127M PHE* 3.6 26.5 - - + -
307M ASN 3.1 18.8 + - - +
308M VAL 3.6 4.9 - - - +
310M ASN* 1.3 77.6 - - - +
312M LEU* 1.3 57.4 + - - +
314M GLY* 3.0 17.8 + - - -
316M CYS* 3.8 24.7 - - - +
317M GLU 4.4 8.1 - - - +
318M PRO* 3.9 13.0 - - - -
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Residues in contact with LEU 312 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5M PRO* 3.7 6.4 - - - +
6M ILE* 3.0 26.5 + - + +
11M ILE* 3.9 37.5 - - + -
13M PHE* 4.3 8.1 - - + -
74M ASP* 6.0 1.3 - - + -
75M ALA* 4.5 7.6 - - + -
98M HIS* 3.4 40.4 - - + +
125M ARG* 4.5 6.5 - - + +
127M PHE* 4.2 18.6 - - + -
308M VAL* 3.2 31.3 + - + +
309M ILE 3.1 5.2 + - - +
311M CYS* 1.3 77.0 - - - +
313M ARG* 1.3 58.1 + - - +
314M GLY 3.0 7.5 + - - -
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Residues in contact with ARG 313 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5M PRO* 4.9 1.8 - - - +
6M ILE 3.4 24.5 - - - +
7M THR* 3.6 45.1 + - + +
9M ARG 4.6 8.9 + - - -
11M ILE* 4.7 6.2 - - + +
35M ARG* 3.7 40.5 + - - +
309M ILE* 3.1 35.1 + - + +
310M ASN* 3.7 10.1 - - - +
311M CYS 3.3 0.4 - - - -
312M LEU* 1.3 75.2 - - - +
314M GLY* 1.3 58.9 + - - +
315M ASP* 3.3 16.1 + - - +
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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