Contacts of the helix formed by residues 351 - 368 (chain A) in PDB entry 5L0T
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 351 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A TRP* 4.6 1.1 - - - -
188A ARG* 3.6 17.3 - - - +
347A ARG 3.0 27.4 + - - +
348A ASN* 3.8 18.5 + - - +
350A LEU* 1.3 81.7 - - - +
352A MET* 1.3 67.7 + - - +
353A ASP* 4.1 14.1 - - + +
354A ASP* 2.9 28.2 + - - +
355A ILE* 3.3 8.3 + - - +
405A CA 4.2 11.6 - - - -
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Residues in contact with MET 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A HIS* 5.0 0.7 - - - +
114A PHE* 4.0 24.2 - - + -
166A PHE 3.3 26.7 - - - +
167A TRP* 3.4 31.4 - - + -
184A TRP* 4.5 9.3 - - - -
185A ASP* 3.6 40.8 - - + +
188A ARG* 4.8 3.0 - - - +
351A GLN* 1.3 72.9 - - - +
353A ASP* 1.3 64.7 + - - +
355A ILE* 3.1 23.4 + - - +
356A THR* 3.2 15.6 + - - +
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Residues in contact with ASP 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLU* 5.5 2.6 - - - +
351A GLN* 3.1 13.5 - - + +
352A MET* 1.3 81.6 - - - +
354A ASP* 1.3 59.1 + - - +
356A THR* 3.5 7.7 + - - +
357A CYS* 2.9 29.7 + - - +
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Residues in contact with ASP 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLN 4.9 2.8 - - - +
53A ASN* 3.6 28.8 + - - +
54A CYS* 3.6 10.1 + - + +
57A TYR* 4.6 6.4 - - + -
300A PHE* 5.2 1.8 - - + -
348A ASN 4.0 2.4 - - - +
349A HIS* 3.2 34.3 + - - +
350A LEU* 4.3 2.2 - - - -
351A GLN* 2.9 38.1 + - - +
353A ASP* 1.3 77.4 - - - +
355A ILE* 1.3 62.1 + - + +
357A CYS* 4.2 4.7 - - - -
358A TYR* 2.9 30.3 + - - +
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Residues in contact with ILE 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE* 3.6 32.8 - - + -
162A PRO* 3.6 23.1 - - + +
166A PHE* 3.6 46.7 - - + -
184A TRP* 4.7 1.1 - - + -
300A PHE* 3.8 18.6 - - + -
350A LEU* 3.9 13.2 - - + -
351A GLN 3.5 13.0 - - - +
352A MET* 3.1 13.6 + - - +
354A ASP* 1.3 77.0 - - - +
356A THR* 1.3 61.9 + - - +
358A TYR* 3.3 3.3 + - - +
359A TRP* 3.1 25.0 + - + -
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Residues in contact with THR 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE* 3.6 24.4 - - + +
117A GLU* 3.9 31.5 + - + +
118A VAL* 3.3 29.2 - - + +
121A ARG* 5.4 2.0 - - - +
352A MET* 3.2 13.9 + - - +
353A ASP* 3.9 10.0 - - - -
355A ILE* 1.3 77.7 - - - +
357A CYS* 1.3 62.9 + - - +
359A TRP* 3.3 6.6 + - - +
360A GLU* 3.0 22.1 + - - +
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Residues in contact with CYS 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASN* 4.3 11.2 - - + -
54A CYS* 2.1 54.3 - - + +
55A SER 4.9 0.4 - - - -
353A ASP 2.9 18.7 + - - +
354A ASP* 4.2 0.9 - - - -
356A THR* 1.3 77.0 - - - +
358A TYR* 1.3 57.0 + - - +
360A GLU* 3.2 8.0 + - - +
361A ASN* 2.9 44.5 + - - +
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Residues in contact with TYR 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A CYS* 3.4 11.1 - - + -
57A TYR* 3.5 37.0 - + + -
60A VAL* 3.3 26.8 - - + +
61A ILE* 3.4 35.2 + - + +
64A ASP* 4.8 0.7 + - - -
160A MET 3.8 21.5 + - - -
162A PRO* 3.8 21.1 - - + -
300A PHE* 3.6 33.6 - + + +
354A ASP 2.9 18.8 + - - +
355A ILE 3.8 4.0 - - - +
356A THR 3.3 0.2 - - - -
357A CYS* 1.3 75.3 - - - +
359A TRP* 1.3 56.8 + - - +
361A ASN* 3.9 1.6 - - - +
362A LEU* 2.8 43.8 + - + +
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Residues in contact with TRP 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A VAL* 3.8 31.0 - - + -
114A PHE* 3.3 43.4 - + + +
115A ILE* 4.1 11.9 - - + -
118A VAL* 4.9 8.3 - - + -
129A ILE* 4.2 12.3 - - + -
148A PHE* 5.2 2.2 - + - -
161A TYR* 3.3 44.6 - + + -
162A PRO* 3.6 30.3 + - + +
355A ILE 3.1 21.2 + - - -
356A THR* 3.5 9.2 - - - +
358A TYR* 1.3 77.6 - - - +
360A GLU* 1.3 62.3 + - - +
362A LEU* 3.8 6.5 - - + +
363A LEU* 3.0 65.7 + - + +
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Residues in contact with GLU 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 3.7 22.5 - - + +
121A ARG* 2.9 57.5 + - + +
122A LEU* 3.9 10.1 - - + +
356A THR* 3.0 13.3 + - - +
357A CYS* 3.6 11.1 - - - +
359A TRP* 1.3 76.9 - - - +
361A ASN* 1.3 65.5 + - - +
364A SER* 2.8 42.1 + - - +
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Residues in contact with ASN 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASN* 5.8 0.2 + - - -
54A CYS* 3.3 26.4 + - - -
55A SER* 5.1 4.8 - - - +
58A HIS* 5.0 12.9 - - + +
61A ILE* 3.8 17.4 - - + +
357A CYS* 2.9 24.8 + - - +
358A TYR 3.9 1.1 - - - +
360A GLU* 1.3 83.0 - - - +
362A LEU* 1.3 64.7 + - - +
364A SER* 3.8 4.3 - - - -
365A GLU* 3.0 31.4 + - + +
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Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 3.7 35.6 - - + +
64A ASP* 5.6 0.7 - - + -
65A LEU* 4.4 7.1 - - + +
148A PHE* 3.7 23.1 - - + -
159A ILE* 3.7 22.4 - - + -
160A MET 3.3 23.8 - - - +
161A TYR* 4.0 15.9 - - + -
162A PRO* 4.9 0.2 - - + -
358A TYR* 2.8 29.4 + - + +
359A TRP* 3.8 12.1 - - + +
361A ASN* 1.3 74.0 - - - +
363A LEU* 1.3 59.6 + - + +
365A GLU* 3.3 1.2 + - - +
366A TYR* 2.9 30.0 + - - +
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Residues in contact with LEU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 4.2 14.6 - - + -
118A VAL* 5.5 0.4 - - + -
122A LEU* 4.0 24.9 - - + -
125A MET* 3.5 27.7 - - + +
127A MET* 4.2 22.0 - - + -
129A ILE* 5.6 0.2 - - + -
148A PHE* 4.0 29.8 - - + -
359A TRP* 3.0 49.2 + - + +
362A LEU* 1.3 77.3 - - + +
364A SER* 1.3 59.5 + - - +
366A TYR* 3.8 2.9 - - + +
367A SER* 2.9 30.5 + - - -
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Residues in contact with SER 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG 4.6 3.5 + - - -
122A LEU* 3.6 15.5 - - - +
123A PRO* 4.4 11.0 - - - +
360A GLU* 2.8 28.5 + - - +
361A ASN* 3.8 5.2 - - - -
363A LEU* 1.3 77.6 - - - +
365A GLU* 1.3 66.1 + - - +
367A SER* 2.8 24.3 + - - -
368A LYS* 3.6 12.7 - - - +
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Residues in contact with GLU 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A HIS* 4.3 18.8 + - + +
61A ILE* 4.1 11.7 - - + -
65A LEU* 3.7 19.1 - - + -
361A ASN* 3.0 22.8 + - + +
362A LEU 3.9 0.4 - - - +
364A SER* 1.3 75.2 - - - +
366A TYR* 1.3 68.6 + - - +
368A LYS* 2.8 52.8 + - - +
369A PHE* 3.9 15.0 - - + -
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Residues in contact with TYR 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 3.6 27.5 - - + +
68A PHE* 6.0 0.2 - + - -
72A ILE* 3.8 21.5 - - + -
77A MET* 3.4 20.1 - - - +
125A MET* 4.2 18.6 - - + -
126A GLU 2.7 29.2 + - - -
127A MET* 3.6 13.8 - - + +
128A VAL 5.0 0.3 + - - -
146A PRO* 4.2 11.3 + - + +
148A PHE* 3.6 37.3 - + + -
159A ILE* 4.2 2.0 - - + -
362A LEU 2.9 18.2 + - - +
363A LEU* 3.8 2.7 - - + +
365A GLU* 1.3 77.9 - - - +
367A SER* 1.3 66.9 + - - +
369A PHE* 2.9 22.4 + - + +
370A LEU* 3.7 18.8 + - + +
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Residues in contact with SER 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PRO* 3.4 21.0 - - - +
124A ASP 4.2 6.1 - - - +
125A MET* 3.7 31.2 - - - -
363A LEU 2.9 15.6 + - - -
364A SER 2.8 18.5 + - - -
365A GLU 3.2 0.2 - - - -
366A TYR* 1.3 82.9 - - - +
368A LYS* 1.3 63.8 + - - +
369A PHE 3.2 0.9 + - - -
370A LEU* 3.4 19.7 + - - +
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Residues in contact with LYS 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A SER* 3.6 15.5 - - - +
365A GLU* 2.8 48.5 + - - +
366A TYR 3.0 1.0 + - - -
367A SER* 1.3 79.2 + - - +
369A PHE* 1.3 71.3 + - + +
370A LEU 3.4 4.7 + - - +
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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