Contacts of the helix formed by residues 348 - 364 (chain A) in PDB entry 4N9W
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 348 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A VAL 3.2 7.0 - - - +
171A ASP* 3.9 7.9 - - - +
172A VAL* 3.1 40.9 + - + +
173A ALA 4.7 1.0 + - - -
344A VAL 3.7 2.8 + - - -
345A HIS* 3.1 19.7 + - + +
347A TYR* 1.3 80.1 - - - +
349A TRP* 1.3 66.8 + - - +
350A SER* 2.7 38.6 + - - +
351A VAL* 3.1 4.9 + - - +
352A VAL* 3.0 18.2 + - - +
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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
----------------------------------------------------------
20A HIS* 3.6 44.2 - + - -
23A GLN* 2.7 46.0 + - + +
24A LEU* 4.0 28.0 - - + -
27A VAL* 3.7 30.3 - - + -
169A GLY* 3.4 24.7 - - - -
170A VAL 3.0 32.0 + - - -
171A ASP* 3.6 15.0 - - + +
348A ASP* 1.3 75.5 - - - +
350A SER* 1.3 55.2 + - - +
352A VAL* 3.8 23.3 - - + +
353A SER* 2.6 40.9 + - - -
356A ILE* 4.3 0.9 - - + -
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Residues in contact with SER 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 6.2 0.2 - - - -
348A ASP* 2.7 24.0 + - - +
349A TRP* 1.3 80.5 - - - +
351A VAL* 1.3 77.8 + - - +
353A SER* 3.5 9.7 + - - -
354A ALA* 3.7 11.8 + - - +
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A HIS 3.8 18.6 - - - +
346A ARG* 4.0 13.2 - - + +
348A ASP 3.1 5.3 + - - +
350A SER* 1.3 87.0 + - - +
352A VAL* 1.3 65.4 + - - +
354A ALA* 3.6 7.0 + - - +
355A GLN* 3.3 33.2 + - - +
402A EDO 4.1 26.0 - - - +
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A HIS* 5.6 0.7 - - + -
166A ILE* 3.9 7.2 - - + -
167A PRO* 3.4 34.5 - - + +
168A ASN* 5.0 0.2 - - - -
169A GLY* 4.2 3.6 - - - +
346A ARG 3.6 19.5 - - - +
347A TYR* 3.9 13.7 - - - +
348A ASP 3.0 17.6 + - - +
349A TRP* 4.0 18.2 - - + +
351A VAL* 1.3 75.3 - - - +
353A SER* 1.3 67.9 + - - +
355A GLN* 3.1 22.1 + - - +
356A ILE* 3.1 26.0 + - + +
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Residues in contact with SER 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.5 7.8 - - - +
27A VAL* 3.8 26.6 - - - +
28A LEU* 5.8 6.3 - - - +
349A TRP* 2.6 30.3 + - - +
350A SER* 3.5 5.4 + - - -
352A VAL* 1.3 79.5 - - - +
354A ALA* 1.3 56.4 + - - +
356A ILE* 3.4 12.7 + - - +
357A MET* 2.9 30.5 + - - +
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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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350A SER 3.7 10.2 + - - +
351A VAL* 3.6 12.3 + - - +
352A VAL 3.2 0.2 - - - -
353A SER* 1.3 82.1 + - - +
355A GLN* 1.3 61.5 + - - +
357A MET* 3.4 7.1 + - - +
358A ARG* 3.1 49.2 + - - +
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Residues in contact with GLN 355 (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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165A GLU 4.2 7.1 + - - -
166A ILE* 3.7 37.9 - - + +
167A PRO* 4.4 7.3 - - - +
346A ARG 4.9 1.4 - - - +
351A VAL* 3.3 33.7 - - + +
352A VAL* 3.1 12.1 + - - +
354A ALA* 1.3 76.6 - - - +
356A ILE* 1.3 61.9 + - - +
358A ARG* 3.3 29.5 + - - +
359A VAL* 3.5 16.5 + - - +
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Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A HIS* 4.5 10.1 - - + +
24A LEU* 3.8 33.0 - - + -
28A LEU* 6.4 0.2 - - + -
92A HIS* 4.3 5.2 - - + -
145A ILE* 4.2 15.5 - - + -
166A ILE* 4.0 20.4 - - + -
349A TRP* 4.3 5.2 - - + -
352A VAL* 3.1 29.5 + - + +
353A SER* 3.7 7.6 - - - +
354A ALA 3.3 0.2 - - - -
355A GLN* 1.3 71.9 - - - +
357A MET* 1.3 66.9 + - - +
359A VAL* 3.1 8.3 + - - +
360A TYR* 3.0 51.4 + - + +
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Residues in contact with MET 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.9 22.9 - - - +
28A LEU* 3.5 26.7 - - + -
33A HIS* 3.5 33.0 - - + +
353A SER 2.9 18.1 + - - +
354A ALA* 3.7 7.6 - - - +
355A GLN 3.3 0.2 - - - -
356A ILE* 1.3 77.5 - - - +
358A ARG* 1.3 58.8 + - + +
360A TYR* 3.1 15.7 + - + +
361A GLU* 2.8 50.6 + - - +
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Residues in contact with ARG 358 (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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354A ALA* 3.1 42.7 + - - +
355A GLN* 3.6 25.0 - - - +
356A ILE 3.2 0.6 - - - -
357A MET* 1.3 76.5 - - + +
359A VAL* 1.3 58.0 + - + +
361A GLU* 3.4 17.6 + - - +
362A THR* 2.9 32.9 + - - -
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Residues in contact with VAL 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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114A VAL* 4.2 27.1 - - + -
143A GLY* 4.3 15.9 - - - -
144A ARG 4.8 1.3 - - - +
145A ILE* 4.2 17.3 - - + -
164A VAL* 3.8 28.9 - - + -
166A ILE* 4.3 0.7 - - + -
355A GLN 3.5 15.9 - - - +
356A ILE 3.1 7.1 + - - +
358A ARG* 1.3 74.5 - - + +
360A TYR* 1.3 67.3 + - + +
362A THR* 3.1 8.0 + - + -
363A VAL* 3.1 28.0 + - + +
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Residues in contact with TYR 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.8 17.9 - - + -
3A ILE* 3.9 31.6 - - + -
5A MET* 3.6 16.8 - - - +
24A LEU* 3.7 5.0 - - - +
28A LEU* 4.1 13.5 - - + -
90A VAL* 3.9 19.0 - - + +
92A HIS* 2.6 47.3 + + + +
114A VAL* 4.1 13.9 - - + -
356A ILE* 3.0 29.4 + - + -
357A MET* 3.4 28.5 - - + +
359A VAL* 1.3 75.8 - - + +
361A GLU* 1.3 59.6 + - - +
363A VAL* 3.3 0.7 + - - -
364A SER* 2.8 30.5 + - - -
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Residues in contact with GLU 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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1A MET* 5.6 3.1 - - - -
357A MET* 2.8 44.1 + - - +
358A ARG* 3.6 19.5 - - - +
360A TYR* 1.3 74.5 - - - +
362A THR* 1.3 63.2 + - - +
364A SER* 3.4 23.0 + - - +
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Residues in contact with THR 362 (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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142A ILE* 6.3 0.7 - - + -
358A ARG* 2.9 15.7 + - - +
359A VAL* 3.4 13.1 - - + +
361A GLU* 1.3 79.1 - - - +
363A VAL* 1.3 66.5 + - + +
364A SER 4.0 3.8 - - - +
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Residues in contact with VAL 363 (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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90A VAL* 5.3 1.6 - - + -
112A PRO* 3.4 42.5 - - + +
113A ILE 3.7 4.9 - - - +
114A VAL* 3.9 11.7 - - + -
142A ILE* 3.5 30.7 - - + +
143A GLY* 3.8 29.6 - - - +
359A VAL* 3.1 18.9 + - + +
360A TYR* 4.0 2.9 - - - +
362A THR* 1.3 81.8 - - + +
364A SER* 1.3 61.1 + - - +
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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
----------------------------------------------------------
1A MET* 4.4 8.2 - - - +
89A ASP* 3.8 24.0 - - - -
90A VAL* 3.9 7.9 - - - +
112A PRO* 4.2 6.7 - - - -
360A TYR 2.8 22.9 + - - -
361A GLU* 3.4 18.1 + - - +
362A THR 4.0 3.6 - - - +
363A VAL* 1.3 81.5 - - - +
365A GLY* 1.3 60.1 + - - +
368A ILE* 5.3 2.2 - - - -
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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