Contacts of the helix formed by residues 341 - 361 (chain A) in PDB entry 1D0L
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 SER 341 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A TYR* 5.0 2.3 + - - -
286A PHE* 3.9 9.9 - - - -
336A THR* 3.8 4.6 - - - +
339A ASN* 2.7 16.2 + - - +
340A HIS* 1.3 74.2 - - - +
342A THR* 1.3 63.3 + - - +
343A HIS* 3.4 8.5 + - - +
344A TYR* 3.1 30.2 + - - +
345A ALA* 3.1 23.0 + - - +
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Residues in contact with THR 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLY* 4.2 4.9 - - - -
286A PHE* 3.2 37.2 + - - +
315A LEU* 4.0 24.2 - - + -
316A ARG 5.6 2.9 - - - +
317A LEU* 4.4 21.1 - - + -
332A PHE* 3.5 15.0 - - + -
341A SER* 1.3 69.3 + - - +
343A HIS* 1.3 65.9 + - + +
345A ALA 3.4 1.0 + - - -
346A MET* 3.0 29.0 + - + +
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Residues in contact with HIS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ALA* 3.9 18.3 - - + +
114A TRP* 3.5 52.6 + + - +
117A TYR* 3.3 34.0 - - + +
316A ARG 5.5 1.4 + - - -
317A LEU* 4.2 14.5 - - + +
318A ASP* 5.3 2.6 + - - +
341A SER* 3.4 7.0 + - - +
342A THR* 1.3 81.1 - - + +
344A TYR* 1.3 63.9 + - - +
346A MET* 3.4 0.6 + - - -
347A ALA* 2.9 26.7 + - - +
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Residues in contact with TYR 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TYR* 3.4 18.3 + - - +
158A ILE* 3.3 16.4 - - + +
161A VAL* 3.6 26.9 - - + -
162A GLU* 2.6 33.8 + - - +
335A ILE* 4.2 15.5 - - + -
338A TYR* 3.3 13.9 - - + -
339A ASN* 3.4 43.7 - - + +
341A SER* 3.1 28.2 + - - +
343A HIS* 1.3 77.8 - - - +
345A ALA* 1.3 62.2 + - - +
347A ALA* 3.2 2.8 + - - +
348A VAL* 2.9 48.2 + - + +
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Residues in contact with ALA 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A PHE* 3.6 24.5 - - + -
335A ILE* 3.5 36.4 - - + +
336A THR* 3.7 15.0 - - + +
341A SER 3.1 11.6 + - - +
344A TYR* 1.3 80.9 - - + +
346A MET* 1.3 61.3 + - - +
348A VAL* 3.4 2.1 + - - +
349A TRP* 3.1 25.3 + - - +
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Residues in contact with MET 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TRP* 3.6 21.1 - - + -
272A ALA* 4.6 1.1 - - + -
315A LEU* 3.9 16.2 - - + -
317A LEU* 3.9 18.4 - - + -
326A TRP* 3.8 31.6 - - + -
332A PHE* 3.7 21.3 - - + -
342A THR 3.0 19.0 + - - +
343A HIS* 3.9 1.3 - - - +
345A ALA* 1.3 76.0 - - - +
347A ALA* 1.3 58.5 + - - +
349A TRP* 3.5 24.9 + - - +
350A GLN* 2.9 63.3 + - - +
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Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TRP* 3.6 10.1 - - + -
117A TYR* 3.6 21.8 - - + -
118A ARG* 5.4 2.5 - - - -
121A PHE* 4.1 18.6 - - + -
122A ILE* 4.4 4.9 - - + +
161A VAL* 4.2 6.9 - - + +
343A HIS 2.9 19.2 + - - +
344A TYR 3.6 3.4 - - - +
346A MET* 1.3 75.4 - - - +
348A VAL* 1.3 59.8 + - - +
350A GLN* 4.8 2.0 - - - -
351A LEU* 2.9 34.0 + - - +
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Residues in contact with VAL 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLU 4.4 1.2 - - - +
154A ILE* 4.0 9.2 - - + +
157A GLY* 3.5 10.4 - - - +
158A ILE* 3.7 38.1 - - + +
161A VAL* 3.8 23.1 - - + -
335A ILE* 4.2 14.4 - - + -
344A TYR* 2.9 50.3 + - + +
345A ALA 3.7 4.7 - - - +
347A ALA* 1.3 76.0 - - - +
349A TRP* 1.3 58.3 + - - +
352A GLY* 3.0 23.6 + - - -
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Residues in contact with TRP 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLU* 5.6 3.8 - - + +
154A ILE* 4.1 16.4 - - + -
271A VAL* 3.7 43.4 - - + +
272A ALA* 3.0 34.8 - - + -
326A TRP* 3.4 32.8 - + - -
332A PHE* 5.3 0.4 - + - -
335A ILE* 4.2 9.9 - - + -
345A ALA 3.1 17.5 + - - +
346A MET* 3.7 20.2 - - - +
348A VAL* 1.3 80.1 - - - +
350A GLN* 1.3 60.6 + - + +
352A GLY* 3.3 2.3 + - - -
353A GLN* 3.0 71.6 + - + +
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Residues in contact with GLN 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TRP* 3.6 16.3 - - - +
118A ARG* 2.8 40.3 + - - +
122A ILE* 3.7 14.6 - - + +
317A LEU* 4.6 0.4 - - - +
324A GLN* 5.1 0.6 + - - -
326A TRP* 3.7 22.4 - - + -
346A MET* 2.9 45.8 + - - +
347A ALA* 4.8 0.4 - - - -
349A TRP* 1.3 80.7 - - + +
351A LEU* 1.3 59.3 + - - +
353A GLN* 3.4 11.9 + - - +
354A ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PHE* 3.7 23.6 - - + +
122A ILE* 3.7 15.8 - - + +
126A ASN* 4.3 10.3 - - + +
127A VAL* 4.3 12.3 - - + -
157A GLY* 3.9 22.4 - - - +
160A GLY* 4.1 1.1 - - - -
161A VAL* 3.9 20.4 - - + +
165A TRP* 4.0 23.1 - - + -
347A ALA 2.9 20.7 + - - +
348A VAL 3.9 2.5 - - - +
350A GLN* 1.3 71.9 - - - +
352A GLY* 1.3 67.5 + - - +
354A ALA* 3.2 2.1 + - - +
355A VAL* 3.0 43.2 + - + +
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Residues in contact with GLY 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TRP* 4.2 0.2 - - - -
153A GLU* 3.2 45.3 - - - +
156A VAL* 5.2 0.9 - - - -
157A GLY* 4.1 5.4 - - - -
348A VAL 3.0 12.4 + - - -
349A TRP 3.7 2.9 - - - -
350A GLN 3.3 0.2 - - - -
351A LEU* 1.3 77.4 - - - +
353A GLN* 1.3 54.9 + - - +
355A VAL* 3.4 7.2 + - - +
356A ALA 3.0 22.3 + - - -
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Residues in contact with GLN 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLU* 4.8 8.1 - - + +
349A TRP* 3.0 68.6 + - + +
350A GLN* 3.7 13.1 - - - +
351A LEU 3.3 0.2 - - - -
352A GLY* 1.3 72.8 - - - +
354A ALA* 1.3 64.8 + - - +
356A ALA* 3.3 7.3 + - - +
357A LEU* 3.0 36.3 + - + +
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Residues in contact with ALA 354 (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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118A ARG* 5.9 1.3 - - - +
122A ILE* 4.4 11.7 - - + -
127A VAL* 3.7 25.0 - - + +
350A GLN 2.9 18.7 + - - +
351A LEU* 3.2 7.4 + - - +
353A GLN* 1.3 75.3 - - - +
355A VAL* 1.3 57.8 + - - +
357A LEU* 3.5 8.9 + - - +
358A ALA* 3.0 29.8 + - - +
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Residues in contact with VAL 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 3.8 29.8 - - - +
130A GLY* 3.5 34.3 - - - +
131A VAL* 3.6 8.2 - - - +
134A TRP* 3.6 22.2 - - + -
156A VAL* 4.1 12.3 - - + -
165A TRP* 4.6 0.7 - - + -
351A LEU* 3.0 30.2 + - + +
352A GLY 3.7 4.5 - - - +
354A ALA* 1.3 75.0 - - - +
356A ALA* 1.3 64.6 + - - +
358A ALA* 3.2 3.2 + - - +
359A ARG* 3.1 22.7 + - + +
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Residues in contact with ALA 356 (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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134A TRP* 3.7 19.7 - - + -
153A GLU* 3.7 22.0 - - - +
352A GLY 3.0 17.2 + - - +
353A GLN* 3.3 8.0 + - - +
355A VAL* 1.3 78.9 - - - +
357A LEU* 1.3 63.4 + - + +
359A ARG* 3.3 16.6 + - - +
360A VAL* 3.6 12.3 - - - +
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Residues in contact with LEU 357 (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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353A GLN* 3.0 27.2 + - + +
354A ALA* 3.9 6.5 - - - +
356A ALA* 1.3 78.2 - - + +
358A ALA* 1.3 62.2 + - - +
359A ARG 3.1 1.2 + - - -
360A VAL* 3.1 17.7 + - + +
361A GLN* 3.0 28.0 + - - +
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Residues in contact with ALA 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 3.6 14.1 - - + -
128A GLN* 6.5 0.7 - - + -
131A VAL* 3.6 26.8 - - + +
354A ALA 3.0 19.1 + - - +
355A VAL 3.2 0.6 + - - +
357A LEU* 1.3 75.6 - - - +
359A ARG* 1.3 60.6 + - - +
361A GLN* 3.6 25.6 - - - +
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Residues in contact with ARG 359 (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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131A VAL* 4.0 24.5 - - + -
134A TRP* 3.3 59.3 - - - +
135A ASN* 3.0 27.3 + - - +
138A GLU* 3.1 32.1 + - - -
355A VAL 3.1 16.1 + - - +
356A ALA 3.4 8.0 + - - +
357A LEU 3.1 0.4 - - - -
358A ALA* 1.3 75.3 - - - +
360A VAL* 1.3 64.3 + - + +
361A GLN 3.2 9.3 + - - +
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Residues in contact with VAL 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ALA 3.6 15.9 - - - +
357A LEU* 3.1 18.1 + - + +
359A ARG* 1.3 78.6 - - + +
361A GLN* 1.3 70.8 + - - +
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Residues in contact with GLN 361 (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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357A LEU* 3.0 26.3 + - - +
358A ALA* 3.6 22.7 - - - +
359A ARG 3.2 8.0 - - - +
360A VAL* 1.3 90.5 - - - +
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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