Contacts of the helix formed by residues 299 - 312 (chain Q) in PDB entry 5KZ5
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 PRO 299 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109K PHE* 3.9 13.5 - - + -
202K SER* 3.7 25.8 - - - +
209K ASP* 3.9 7.4 - - - +
210K ALA* 3.3 9.8 - - - +
77Q MET* 4.0 4.2 - - + +
81Q LEU* 4.5 3.8 - - + -
84Q TYR* 3.6 18.1 - - + +
85Q TYR* 3.3 30.3 - - + +
297Q PRO* 3.6 7.6 - - + -
298Q THR* 1.3 92.0 - - - +
300Q LEU* 1.3 60.0 + - + +
302Q VAL* 3.5 4.6 + - + +
303Q GLY 3.1 22.2 + - - -
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Residues in contact with LEU 300 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109K PHE* 5.9 3.8 - - + -
113K LEU* 6.5 0.7 - - + -
116K LYS* 3.9 25.1 - - - +
199K ASP* 6.2 2.0 - - + -
202K SER* 3.8 22.7 - - - +
210K ALA* 3.9 4.9 - - - +
262Q PRO* 3.6 32.3 - - + +
264Q GLY 6.0 0.9 - - - -
265Q VAL* 4.2 23.1 - - + -
297Q PRO* 3.9 30.5 - - + +
298Q THR 3.3 0.6 - - - -
299Q PRO* 1.3 77.2 - - + +
301Q VAL* 1.4 59.3 + - + +
303Q GLY* 3.4 0.7 + - - -
304Q LEU* 3.1 31.4 + - - +
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Residues in contact with VAL 301 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103Q MET* 4.7 15.9 - - + +
106Q ALA* 3.6 9.3 - - + +
107Q ARG* 3.6 35.7 - - + +
110Q VAL* 3.7 22.0 - - + +
123Q PHE* 5.4 12.8 - - + -
296Q VAL* 5.4 2.9 - - + -
297Q PRO* 3.5 20.4 - - + +
298Q THR* 3.3 8.9 + - + +
300Q LEU* 1.4 74.7 - - + +
302Q VAL* 1.4 64.3 + - - +
304Q LEU* 4.9 0.4 - - - -
305Q GLY* 3.1 20.3 + - - -
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Residues in contact with VAL 302 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J THR* 5.1 6.7 - - - +
77Q MET* 3.9 19.5 - - + -
81Q LEU* 6.0 0.4 - - + -
84Q TYR* 4.0 9.2 - - + +
102Q ALA* 4.9 4.0 - - + +
106Q ALA* 3.6 23.3 - - + -
298Q THR* 3.3 28.0 + - + +
299Q PRO 3.7 8.1 - - - +
301Q VAL* 1.4 74.4 - - - +
303Q GLY* 1.4 57.1 + - - +
306Q ALA* 3.0 32.6 + - + +
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Residues in contact with GLY 303 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J ALA* 4.5 2.3 - - - -
49J THR* 4.3 11.6 + - - -
210K ALA* 3.4 32.3 - - - -
77Q MET* 4.6 0.9 - - - +
259Q ILE* 6.0 0.6 - - - +
262Q PRO* 6.1 0.9 - - - -
299Q PRO 3.1 13.0 + - - -
300Q LEU 3.9 1.3 - - - -
302Q VAL* 1.4 75.2 - - - +
304Q LEU* 1.3 62.2 + - - +
306Q ALA* 4.3 0.3 - - - +
307Q ALA* 3.3 24.6 + - - +
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Residues in contact with LEU 304 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210K ALA* 5.1 0.6 - - - +
110Q VAL* 3.6 24.9 - - + -
237Q VAL* 4.2 15.3 - - + -
254Q ILE* 5.1 15.9 - - + -
259Q ILE* 4.0 28.2 - - + +
262Q PRO* 5.8 2.5 - - + +
265Q VAL* 6.5 0.9 - - + -
269Q TYR* 5.1 7.2 - - - +
300Q LEU 3.1 17.1 + - - +
301Q VAL* 4.9 0.2 - - - -
303Q GLY* 1.3 73.3 - - - +
305Q GLY* 1.3 62.3 + - - +
307Q ALA* 3.6 5.9 + - + +
308Q CYS* 3.2 39.8 + - - -
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Residues in contact with GLY 305 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106Q ALA* 4.4 2.0 - - - -
109Q GLN* 3.7 34.6 - - - +
110Q VAL* 3.5 8.2 - - - +
301Q VAL 3.1 18.3 + - - -
302Q VAL 4.0 0.2 - - - -
304Q LEU* 1.3 74.7 - - - +
306Q ALA* 1.3 63.3 + - - +
308Q CYS* 3.4 8.0 + - - +
309Q GLU* 3.1 18.0 + - - +
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Residues in contact with ALA 306 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J THR* 3.4 28.3 - - - +
50J CYS 5.0 0.4 - - - +
51J THR* 4.8 14.4 - - + -
109Q GLN* 4.9 2.1 + - - -
302Q VAL* 3.0 22.7 + - + +
305Q GLY* 1.3 74.4 - - - +
307Q ALA* 1.3 62.1 + - - +
309Q GLU* 3.3 12.6 + - + +
310Q VAL* 3.2 28.9 + - - +
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Residues in contact with ALA 307 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J ILE* 3.5 32.0 - - - +
47J ASP* 4.0 3.6 - - - -
48J ALA 3.7 28.6 + - - +
259Q ILE* 5.9 3.6 - - + -
303Q GLY 3.3 18.4 + - - +
304Q LEU* 3.7 8.7 - - + +
305Q GLY 3.3 0.6 - - - -
306Q ALA* 1.3 78.1 - - - +
308Q CYS* 1.4 61.4 + - - +
310Q VAL* 3.7 2.1 + - - +
311Q ALA* 3.4 17.5 + - - +
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Residues in contact with CYS 308 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109Q GLN* 5.5 8.1 - - + +
110Q VAL* 6.0 2.0 - - - -
237Q VAL* 6.0 2.5 - - - -
241Q PRO* 6.2 3.8 - - - -
304Q LEU* 3.2 29.1 + - - -
305Q GLY* 3.4 9.4 + - - +
306Q ALA 3.4 0.2 - - - -
307Q ALA* 1.4 76.6 - - - +
309Q GLU* 1.3 65.7 + - - +
311Q ALA* 3.4 3.9 + - - -
312Q GLN* 2.9 41.7 + - - +
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Residues in contact with GLU 309 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4522 ILE* 4.0 14.1 - - + +
4532 LYS* 3.5 40.8 + - - +
4542 TRP* 3.9 37.1 - - + -
51J THR* 4.4 5.5 - - - +
52J PRO* 3.7 16.0 - - + +
109Q GLN* 4.2 17.4 + - + +
305Q GLY 3.1 13.0 + - - +
306Q ALA* 3.3 15.7 + - - +
308Q CYS* 1.3 75.9 - - - +
310Q VAL* 1.4 56.9 + - + +
312Q GLN* 3.4 3.1 + - - +
313Q GLN* 3.1 29.0 + - + +
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Residues in contact with VAL 310 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J THR* 4.5 10.8 - - + +
45J ASP 3.7 23.6 - - - +
46J ILE* 4.2 7.1 - - + +
48J ALA 5.3 0.2 - - - +
50J CYS 3.1 34.5 - - - +
51J THR* 3.8 12.1 - - - -
52J PRO* 4.0 8.1 - - + -
55J ALA* 5.1 6.7 - - + -
306Q ALA 3.2 16.3 + - - +
307Q ALA* 3.9 5.8 - - - +
309Q GLU* 1.4 72.6 - - + +
311Q ALA* 1.4 62.1 + - - +
313Q GLN* 3.4 18.2 + - - +
314Q GLU* 3.5 23.1 + - - +
318Q ASP* 5.4 0.5 - - - +
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Residues in contact with ALA 311 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J ILE* 3.7 29.4 - - + +
238Q GLY 5.1 2.9 - - - +
240Q ILE 6.2 1.6 - - - -
241Q PRO* 6.0 1.3 - - + -
307Q ALA 3.4 12.7 + - - +
308Q CYS* 3.4 12.3 - - - +
309Q GLU 3.3 0.2 - - - -
310Q VAL* 1.4 78.5 - - - +
312Q GLN* 1.4 71.9 + - - +
315Q MET* 3.2 30.7 + - - +
318Q ASP* 4.7 4.7 - - - +
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Residues in contact with GLN 312 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4542 TRP* 5.7 9.4 - - + -
140N ARG* 4.1 10.5 + - - +
169N GLU* 3.0 25.3 - - - +
241Q PRO* 3.6 37.4 - - + +
308Q CYS* 2.9 34.3 + - - +
309Q GLU* 3.4 4.2 + - - +
310Q VAL 3.3 0.2 - - - -
311Q ALA* 1.4 100.0 + - - +
313Q GLN* 1.4 57.5 + - - +
314Q GLU 3.7 0.2 - - - -
315Q MET* 3.5 30.6 - - - +
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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