Contacts of the helix formed by residues 314 - 327 (chain I) in PDB entry 5TJ4
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 ASP 314 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310I GLU 4.6 0.4 + - - -
311I LEU* 2.9 17.0 + - + +
312I ALA 3.6 6.6 - - - +
313I LYS* 1.3 77.8 - - - +
315I PRO* 1.4 73.0 - - - +
316I ARG* 2.7 68.7 + - - +
317I ILE* 3.4 13.9 + - + +
318I ALA* 3.4 16.2 + - - +
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Residues in contact with PRO 315 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244I VAL 4.8 2.0 - - - +
313I LYS 3.5 6.9 - - - +
314I ASP* 1.4 90.1 - - - +
316I ARG* 1.3 60.4 + - + +
318I ALA* 3.4 9.7 + - + +
319I ALA* 3.0 26.3 + - - +
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Residues in contact with ARG 316 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232I TRP* 3.5 50.6 - - + +
236I ASP* 3.6 13.5 + - - -
242I TYR* 2.6 47.9 + - + -
243I GLY* 6.4 0.2 - - - -
244I VAL* 3.7 23.7 - - + +
298I PRO* 5.3 5.5 - - - +
314I ASP* 2.7 36.1 + - - +
315I PRO* 1.3 73.0 - - + +
317I ILE* 1.3 58.5 + - - +
319I ALA* 3.4 3.7 + - - +
320I THR* 3.0 28.9 + - - -
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Residues in contact with ILE 317 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232I TRP* 4.0 21.1 - - + -
294I ASN* 5.9 1.3 - - - +
298I PRO* 6.0 1.3 - - + -
300I GLY* 3.5 30.1 - - - +
301I ALA* 4.0 25.8 - - + +
308I GLU* 4.2 11.2 - - - +
311I LEU* 3.5 34.5 - - + +
312I ALA* 4.5 5.2 - - - -
314I ASP* 3.4 18.3 + - + +
315I PRO 3.3 0.4 - - - -
316I ARG* 1.3 73.6 - - - +
318I ALA* 1.3 60.8 + - - +
320I THR* 3.1 8.0 + - - -
321I MET* 2.9 30.3 + - + +
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Residues in contact with ALA 318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312I ALA 4.9 7.3 + - - +
314I ASP 3.4 10.1 + - - +
315I PRO* 3.5 13.2 - - + +
316I ARG 3.3 0.4 - - - -
317I ILE* 1.3 79.1 - - - +
319I ALA* 1.3 57.4 + - - +
321I MET* 3.3 6.9 + - - +
322I GLU* 3.0 28.6 + - - +
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Residues in contact with ALA 319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I SER* 4.4 0.2 - - - -
244I VAL* 3.4 39.0 - - + +
245I THR* 4.0 9.4 - - - +
246I VAL* 4.9 1.9 - - - +
315I PRO 3.0 11.2 + - - +
316I ARG 3.4 9.6 - - - +
318I ALA* 1.3 74.7 - - - +
320I THR* 1.3 63.8 + - - +
322I GLU* 3.4 7.1 + - - +
323I ASN* 2.9 31.3 + - - -
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Residues in contact with THR 320 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I VAL* 4.6 10.3 - - + +
112I ALA* 3.8 31.0 + - + +
114I SER* 3.3 19.3 + - - -
229I PRO* 4.2 11.1 - - + +
232I TRP* 3.6 18.0 - - - -
301I ALA 5.0 5.8 - - - +
316I ARG 3.0 13.9 + - - -
317I ILE* 3.1 12.5 + - - +
319I ALA* 1.3 75.8 - - - +
321I MET* 1.3 64.1 + - + +
323I ASN* 3.2 5.8 + - - +
324I ALA* 2.8 26.3 + - + +
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Residues in contact with MET 321 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I PHE* 5.4 11.4 - - + -
110I VAL* 4.8 13.2 - - + -
301I ALA* 3.8 28.9 - - + -
308I GLU* 5.1 4.0 - - - +
317I ILE* 2.9 26.1 + - + +
318I ALA* 3.9 6.3 - - - +
320I THR* 1.3 73.9 - - - +
322I GLU* 1.3 57.4 + - - +
324I ALA* 3.6 14.6 - - + +
325I GLN* 2.8 52.1 + - + +
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Residues in contact with GLU 322 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246I VAL* 3.9 21.7 - - + +
318I ALA 3.0 16.7 + - - +
319I ALA* 3.6 7.4 - - - +
320I THR 3.3 0.2 - - - -
321I MET* 1.3 76.0 - - - +
323I ASN* 1.3 57.6 + - - +
325I GLN* 3.5 10.9 + - - +
326I LYS* 3.1 26.5 + - - +
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Residues in contact with ASN 323 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112I ALA* 4.9 1.3 - - + -
113I LEU 3.3 20.9 - - - +
114I SER* 3.4 17.2 + - - +
245I THR 3.3 21.8 + - - -
246I VAL* 3.4 8.5 - - - +
247I LEU* 2.9 32.0 + - - +
255I SER 5.4 1.4 - - - +
257I PRO* 3.6 15.0 - - + +
319I ALA 2.9 21.8 + - - -
320I THR 3.5 6.1 - - - +
322I GLU* 1.3 74.1 - - - +
324I ALA* 1.3 65.5 + - - +
326I LYS* 3.1 8.1 + - - +
327I GLY 2.9 19.9 + - - -
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Residues in contact with ALA 324 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I VAL* 4.9 7.9 - - + -
112I ALA* 4.0 9.3 - - + +
259I VAL* 3.6 29.3 - - + +
320I THR* 2.8 19.9 + - + +
321I MET* 3.3 24.2 + - + +
323I ASN* 1.3 72.6 - - - +
325I GLN* 1.3 62.5 + - - +
327I GLY 3.3 18.7 + - - +
328I GLU 5.3 0.2 - - - -
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Residues in contact with GLN 325 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321I MET* 2.8 39.8 + - + +
322I GLU* 3.6 9.5 + - - +
323I ASN 3.2 0.2 - - - -
324I ALA* 1.3 76.3 - - - +
326I LYS* 1.3 61.5 + - - +
327I GLY 3.3 8.0 - - - +
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Residues in contact with LYS 326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254I PRO* 4.2 22.5 - - + +
255I SER 3.9 16.6 - - - +
256I LYS* 3.6 17.3 - - - +
322I GLU 3.1 13.5 + - - +
323I ASN* 3.1 12.6 + - - +
325I GLN* 1.3 74.8 - - - +
327I GLY* 1.3 59.4 + - - +
328I GLU* 5.5 1.0 - - - +
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Residues in contact with GLY 327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256I LYS* 3.7 14.6 - - - -
257I PRO* 3.4 18.1 - - - +
259I VAL* 4.8 0.4 - - - -
323I ASN 2.9 10.8 + - - -
324I ALA 3.3 15.4 + - - +
325I GLN 3.2 6.1 - - - +
326I LYS* 1.3 79.6 - - - +
328I GLU* 1.3 68.9 + - - +
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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