Contacts of the helix formed by residues 299 - 312 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G THR* 4.7 2.1 + - - -
109H PHE* 5.2 13.7 - - + -
202H SER* 5.9 1.1 - - - +
210H ALA* 4.1 20.7 - - + +
84T TYR* 3.4 31.4 - - + +
85T TYR* 3.3 26.5 - - + +
262T PRO* 3.6 11.2 - - + +
297T PRO* 3.6 6.5 - - + -
298T THR* 1.3 89.1 - - - +
300T LEU* 1.4 64.1 + - + +
302T VAL* 3.7 4.5 - - + +
303T GLY* 3.0 24.3 + - - -
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Residues in contact with LEU 300 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109H PHE* 5.9 7.4 - - + -
116H LYS* 3.7 28.7 - - - +
123T PHE* 4.9 2.7 - - + -
262T PRO* 3.9 25.5 - - + +
263T LYS 4.8 7.0 - - - +
264T GLY 5.6 0.7 - - - +
265T VAL* 4.0 36.8 - - + -
297T PRO* 3.9 35.0 - - + +
298T THR 3.2 0.4 - - - -
299T PRO* 1.4 79.6 - - + +
301T VAL* 1.4 64.9 + - + +
303T GLY* 3.5 1.4 + - - -
304T LEU* 3.2 31.9 + - - +
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Residues in contact with VAL 301 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103T MET 5.4 0.4 - - - +
106T ALA* 3.5 36.2 - - + +
107T ARG* 3.9 5.4 - - + +
110T VAL* 3.9 20.5 - - + +
123T PHE* 6.4 2.2 - - + -
296T VAL* 5.9 5.2 - - + -
297T PRO 3.7 18.2 - - - +
298T THR* 3.3 7.8 + - - +
300T LEU* 1.4 74.2 - - + +
302T VAL* 1.4 60.1 + - - +
304T LEU* 3.8 1.5 + - - +
305T GLY* 3.1 25.6 + - - -
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Residues in contact with VAL 302 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G THR* 3.6 21.3 + - + +
121L GLU* 3.3 43.5 - - + +
84T TYR* 4.4 2.9 - - - +
102T ALA 4.6 1.8 - - - +
105T ARG* 5.3 2.0 - - - +
106T ALA* 3.6 23.6 - - + +
298T THR* 3.1 31.9 + - + +
299T PRO* 3.7 6.5 - - + +
301T VAL* 1.4 73.1 - - - +
303T GLY* 1.3 60.3 + - - +
306T ALA* 2.9 38.2 + - + +
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Residues in contact with GLY 303 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G ASP* 4.4 8.4 - - - +
48G ALA* 4.4 2.3 - - - -
49G THR* 3.7 17.9 - - - -
259T ILE* 4.3 7.2 - - - +
262T PRO* 4.1 13.5 - - - -
299T PRO 3.0 17.2 + - - -
300T LEU 4.0 1.6 - - - -
301T VAL 3.3 0.2 - - - -
302T VAL* 1.3 78.2 - - - +
304T LEU* 1.3 62.0 + - - +
307T ALA* 3.7 18.2 - - - +
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Residues in contact with LEU 304 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110T VAL* 5.1 6.3 - - + -
237T VAL* 4.9 4.7 - - + -
254T ILE* 4.0 39.5 - - + -
255T SER 4.9 9.4 - - - +
256T GLY* 5.0 4.3 - - - +
259T ILE* 3.8 26.7 - - + -
262T PRO* 5.0 3.1 - - + +
265T VAL* 4.3 21.1 - - + +
266T GLY* 6.1 2.7 - - - -
269T TYR* 4.5 6.1 - - - +
300T LEU* 3.2 24.7 + - - +
301T VAL* 4.4 2.5 - - - +
303T GLY* 1.3 77.1 - - - +
305T GLY* 1.4 62.4 + - - +
307T ALA* 4.2 7.1 + - - +
308T CYS* 4.7 9.9 - - - -
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Residues in contact with GLY 305 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106T ALA 5.2 0.9 - - - -
109T GLN* 4.3 20.7 - - - +
110T VAL* 3.7 22.1 - - - +
301T VAL 3.1 13.4 + - - -
304T LEU* 1.4 76.8 - - - +
306T ALA* 1.3 63.6 + - - +
307T ALA 3.4 0.7 + - - -
308T CYS* 3.9 10.7 + - - +
309T GLU* 4.1 5.4 + - - +
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Residues in contact with ALA 306 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G THR* 5.3 4.0 - - - -
50G CYS 4.9 4.3 - - - +
121L GLU* 3.4 24.7 - - - +
105T ARG* 3.5 18.6 - - - +
106T ALA* 6.2 1.8 - - - +
109T GLN* 5.1 3.3 - - - +
301T VAL 4.6 0.2 + - - -
302T VAL* 2.9 27.0 + - + +
305T GLY* 1.3 69.7 - - - -
307T ALA* 1.4 62.8 + - - +
308T CYS 3.4 0.2 - - - -
309T GLU* 3.3 10.5 + - - +
310T VAL* 3.2 27.2 + - + +
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Residues in contact with ALA 307 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G ASP* 3.2 19.6 - - - +
46G ILE* 3.8 3.6 - - - +
47G ASP* 3.5 28.5 - - - +
48G ALA 3.6 26.4 + - - +
50G CYS 5.8 0.2 - - - +
303T GLY 3.7 14.9 + - - +
304T LEU 4.4 4.5 - - - +
305T GLY 3.3 1.2 - - - -
306T ALA* 1.4 77.1 - - - +
308T CYS* 1.4 57.7 + - - +
310T VAL* 5.0 0.4 - - - -
311T ALA 3.2 20.6 + - - -
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Residues in contact with CYS 308 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G ILE* 4.6 17.0 - - - +
238T GLY* 5.3 7.9 - - - -
241T PRO* 5.6 11.2 - - - -
304T LEU 4.7 9.9 - - - -
305T GLY 3.9 7.0 + - - +
306T ALA 3.4 0.2 - - - -
307T ALA* 1.4 77.3 - - - +
309T GLU* 1.3 63.2 + - - +
311T ALA* 3.4 19.2 + - - +
312T GLN* 3.9 7.1 + - - +
315T MET* 5.8 1.6 - - - +
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Residues in contact with GLU 309 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4501 LYS* 3.4 11.8 + - - +
4571 HIS* 3.8 30.4 + - - -
281M LEU* 3.7 19.7 - - + +
105T ARG* 3.2 30.1 + - - -
109T GLN* 3.5 30.7 + - + +
305T GLY 4.1 6.1 + - - +
306T ALA* 3.3 13.1 + - - +
308T CYS* 1.3 75.9 - - - +
310T VAL* 1.4 65.0 + - + +
312T GLN* 3.4 23.1 - - - +
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Residues in contact with VAL 310 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4491 LEU* 3.5 20.3 - - - +
4501 LYS* 4.5 6.3 - - - +
45G ASP* 3.6 28.5 - - - +
50G CYS* 3.5 27.4 - - + +
51G THR 3.6 27.6 - - - +
52G PRO* 4.2 11.4 - - + -
55G ALA* 3.7 11.3 - - + +
105T ARG* 5.7 2.2 - - - +
306T ALA* 3.2 17.2 + - + +
309T GLU* 1.4 80.8 - - + +
311T ALA* 1.4 63.2 + - - +
312T GLN 3.4 1.2 + - - +
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Residues in contact with ALA 311 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G THR* 3.7 18.3 - - + +
45G ASP* 3.1 27.4 - - - +
46G ILE* 3.9 15.9 - - + -
307T ALA 3.2 6.4 + - - +
308T CYS* 3.4 15.5 - - - +
309T GLU 3.3 0.6 - - - -
310T VAL* 1.4 76.1 - - - +
312T GLN* 1.4 64.1 + - - +
313T GLN* 3.3 7.8 + - - +
314T GLU 4.4 2.8 + - - -
315T MET* 4.7 12.7 + - + +
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Residues in contact with GLN 312 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4491 LEU* 3.8 11.4 - - - +
4501 LYS* 3.4 24.9 + - - -
136M LYS* 5.5 0.2 - - - +
140M ARG* 3.5 25.6 - - - +
165M SER* 3.6 10.3 + - - -
166M LEU* 3.5 20.5 - - - +
169M GLU* 3.2 23.3 + - - +
308T CYS 3.9 4.6 + - - +
309T GLU* 3.4 17.7 + - - +
310T VAL 3.8 0.3 - - - +
311T ALA* 1.4 75.9 - - - +
313T GLN* 1.4 63.0 + - - +
315T MET* 4.3 21.3 - - + -
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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