Contacts of the helix formed by residues 335 - 352 (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 GLN 335 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I GLN* 5.0 1.8 - - - +
169I PHE* 3.7 25.5 - - + -
178I ILE* 3.9 21.6 - - + +
333I ILE* 3.1 13.5 - - + +
334I PRO* 1.3 93.4 - - - +
336I MET* 1.3 59.4 + - - +
337I SER 3.2 0.4 - - - -
338I ALA* 2.9 21.9 + - - +
339I PHE 3.0 9.9 + - - -
1221I SER* 3.3 38.8 + - - +
1224I LEU* 3.9 28.6 + - + +
1225I ASP* 3.9 9.5 - - - +
1227I HIS* 5.6 3.2 - - - -
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Residues in contact with MET 336 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I ASP* 4.1 16.6 - - + +
168I ALA* 3.7 17.3 - - + -
169I PHE* 3.5 30.2 - - + -
258I PHE* 4.7 2.0 - - + -
330I MET* 5.0 4.3 - - - -
331I PRO* 3.3 59.2 - - + +
333I ILE* 3.5 15.2 - - + +
334I PRO 3.1 0.6 - - - -
335I GLN* 1.3 74.3 - - - +
337I SER* 1.3 66.1 + - - +
339I PHE* 3.2 16.4 + - + +
340I TRP* 2.9 47.0 + - + -
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Residues in contact with SER 337 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I ARG* 4.6 31.9 + - - +
69I GLY* 5.5 4.0 - - - -
334I PRO* 3.4 14.9 + - - +
335I GLN 3.2 0.2 - - - -
336I MET* 1.3 76.7 - - - +
338I ALA* 1.3 64.2 + - - +
340I TRP* 3.3 4.6 + - - +
341I TYR* 3.0 24.4 + - - +
1224I LEU* 5.5 6.9 - - - +
1365I VAL* 5.6 12.1 - - - -
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Residues in contact with ALA 338 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334I PRO 4.5 0.4 + - - -
335I GLN 2.9 11.9 + - - +
337I SER* 1.3 80.8 - - - +
339I PHE* 1.3 62.8 + - - +
341I TYR* 3.4 4.3 + - - +
342I ALA* 3.1 25.6 + - - +
368I ALA* 3.9 5.4 - - - +
1220I MET* 3.6 37.0 - - + -
1221I SER* 3.6 18.4 - - - +
1224I LEU* 4.3 5.1 - - + +
1361I GLN* 4.4 2.9 + - - +
1365I VAL* 6.0 3.1 - - - -
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Residues in contact with PHE 339 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158I TRP* 3.6 37.2 - + - -
168I ALA* 3.5 33.9 - - + -
169I PHE* 4.0 16.2 - - + -
181I VAL* 4.7 5.6 - - + -
183I VAL* 3.8 10.3 - - + -
258I PHE* 3.8 17.3 - + - -
335I GLN 3.0 10.5 + - - +
336I MET* 3.5 16.4 - - - +
338I ALA* 1.3 77.8 - - - +
340I TRP* 1.3 105.8 + + - +
342I ALA* 3.2 2.1 + - - +
343I VAL* 3.1 43.7 + - + +
368I ALA* 4.3 11.8 - - + +
1221I SER* 4.7 0.4 + - - -
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Residues in contact with TRP 340 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I ASP* 3.1 27.4 + - - -
66I ARG* 4.6 7.0 - - - +
154I PRO* 3.6 28.7 - - + +
155I TYR* 3.7 34.8 - + - -
158I TRP* 4.7 6.5 - + + -
258I PHE* 3.6 33.7 - + + -
330I MET* 3.8 15.9 - - + -
336I MET* 2.9 39.3 + - + +
337I SER 3.8 3.6 - - - +
339I PHE* 1.3 94.0 - + - +
341I TYR* 1.3 64.2 + - - +
343I VAL* 3.3 3.4 + - + +
344I ARG* 2.9 29.6 + - - +
2S GLC 3.6 35.1 - - - +
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Residues in contact with TYR 341 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I GLU* 6.0 1.1 - - - -
337I SER 3.0 17.0 + - - +
338I ALA* 4.0 4.3 - - - +
340I TRP* 1.3 75.9 - - - +
342I ALA* 1.3 63.1 + - - +
344I ARG* 3.4 33.3 + - - +
345I THR* 3.2 39.3 + - - -
1360I ASP* 4.8 5.3 + - + +
1361I GLN* 3.0 42.0 - - + +
1364I SER* 3.2 33.9 + - - -
1365I VAL* 5.4 10.1 - - + -
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Residues in contact with ALA 342 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338I ALA 3.1 17.3 + - - +
339I PHE 3.5 4.3 - - - +
341I TYR* 1.3 78.4 - - - +
343I VAL* 1.3 62.6 + - + +
345I THR* 3.6 3.5 + - - -
346I ALA* 3.1 22.2 + - - +
364I ALA* 3.5 36.0 - - + +
368I ALA* 3.8 8.5 - - + -
1361I GLN* 3.6 25.1 - - - +
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Residues in contact with VAL 343 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154I PRO* 3.7 20.9 - - + -
158I TRP* 4.4 17.5 - - + -
161I ILE* 4.9 3.1 - - + -
183I VAL* 3.9 17.5 - - + -
339I PHE* 3.1 45.6 + - + +
340I TRP* 3.8 4.5 - - + +
342I ALA* 1.3 75.3 - - + +
344I ARG* 1.3 68.2 + - - +
346I ALA* 2.9 7.4 + - + -
347I VAL* 2.8 37.5 + - + +
361I LEU* 6.0 4.0 - - + -
364I ALA* 4.7 2.5 - - + -
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Residues in contact with ARG 344 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I GLU* 5.5 3.6 + - - -
45I GLU* 4.9 11.6 + - - -
66I ARG* 4.4 6.7 - - - +
152I GLN 3.8 17.8 - - - +
153I GLU* 3.1 33.5 + - - -
154I PRO* 3.8 16.6 - - + +
340I TRP* 2.9 20.7 + - - +
341I TYR* 3.5 48.5 - - - +
343I VAL* 1.3 76.6 - - - +
345I THR* 1.3 63.5 + - - +
347I VAL* 3.6 2.7 + - - +
348I ILE* 3.1 37.2 + - + +
2S GLC 3.4 25.5 + - - -
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Residues in contact with THR 345 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341I TYR* 3.2 29.1 + - - -
342I ALA 3.6 9.0 - - - +
344I ARG* 1.3 76.7 - - - +
346I ALA* 1.3 67.4 - - - +
348I ILE* 3.1 6.2 + - - +
349I ASN* 2.8 49.4 + - - +
355I GLN* 4.8 1.6 - - - +
1357I LEU* 4.2 18.4 - - + -
1361I GLN* 4.4 9.6 + - - +
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Residues in contact with ALA 346 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192I LEU* 4.9 2.0 - - + -
342I ALA 3.1 11.2 + - - +
343I VAL* 2.9 10.4 + - + +
345I THR* 1.3 80.6 - - - +
347I VAL* 1.3 60.1 + - + +
349I ASN* 3.5 1.5 + - - -
350I ALA* 2.9 31.8 + - - +
355I GLN* 5.0 0.7 - - - -
360I ALA* 3.6 38.2 - - + +
361I LEU* 4.3 11.9 - - + +
364I ALA* 3.8 10.3 - - + -
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Residues in contact with VAL 347 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151I LEU* 4.0 15.9 - - + +
154I PRO* 4.9 4.3 - - + -
157I THR* 3.9 31.2 - - + +
161I ILE* 4.0 22.4 - - + -
192I LEU* 4.3 13.9 - - + +
195I LEU* 4.4 10.8 - - + -
343I VAL* 2.8 39.1 + - + +
344I ARG* 3.9 4.5 - - - +
346I ALA* 1.3 72.6 - - + +
348I ILE* 1.3 57.3 + - - +
350I ALA* 3.3 2.1 + - - +
351I ALA* 2.9 33.3 + - + +
361I LEU* 6.3 0.4 - - + -
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Residues in contact with ILE 348 (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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151I LEU 4.6 8.1 - - - +
152I GLN* 3.8 44.9 - - + +
344I ARG* 3.1 26.2 + - + +
345I THR* 3.1 6.9 + - - +
347I VAL* 1.3 75.6 - - + +
349I ASN* 1.3 63.1 + - - +
351I ALA* 3.4 5.5 + - - +
352I SER* 2.8 41.8 + - - +
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Residues in contact with ASN 349 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345I THR* 2.8 34.1 + - - +
346I ALA 3.8 2.5 - - - +
348I ILE* 1.3 85.4 - - - +
350I ALA* 1.3 56.9 + - - +
352I SER* 3.6 5.5 + - - -
353I GLY 3.2 4.2 + - - -
354I ARG* 3.0 39.4 + - + +
355I GLN* 2.8 44.9 + - + +
360I ALA* 4.8 0.2 - - + -
1357I LEU* 4.1 10.3 - - - +
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Residues in contact with ALA 350 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192I LEU* 4.1 17.9 - - + -
196I VAL* 3.7 33.9 - - + +
346I ALA 2.9 18.3 + - - +
347I VAL 3.8 2.5 - - - +
349I ASN* 1.3 73.7 - - - +
351I ALA* 1.3 65.1 + - - +
353I GLY* 3.4 10.2 + - - -
355I GLN 3.6 14.7 - - - +
357I VAL* 4.3 9.8 - - + +
360I ALA* 4.3 8.0 - - + +
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Residues in contact with ALA 351 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151I LEU* 5.4 4.9 - - + -
192I LEU* 5.8 0.2 - - - +
195I LEU* 5.8 2.7 - - + -
196I VAL* 4.4 7.7 - - + +
199I ILE* 3.6 38.5 - - + +
206I ALA* 3.8 21.8 - - + +
347I VAL* 2.9 23.1 + - + +
348I ILE* 3.7 5.8 - - - +
350I ALA* 1.3 77.6 - - - +
352I SER* 1.3 60.6 + - - +
353I GLY 3.3 1.0 + - - -
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Residues in contact with SER 352 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206I ALA* 4.6 7.9 - - - -
348I ILE* 2.8 31.1 + - - +
349I ASN* 3.5 14.2 + - - -
351I ALA* 1.3 72.6 - - - +
353I GLY* 1.3 57.6 + - - +
354I ARG* 3.2 12.6 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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