Contacts of the helix formed by residues 335 - 348 (chain A) in PDB entry 5NDD
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 LEU 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A VAL* 4.4 12.1 - - + -
84A ILE* 6.0 3.1 - - + -
85A VAL* 3.7 22.9 - - + -
298A ILE* 4.3 14.1 - - + -
299A CYS* 3.9 7.2 - - - -
331A CYS 4.7 0.9 - - - +
332A LEU* 3.3 44.2 - - + +
333A SER 3.1 1.0 - - - -
334A THR* 1.3 74.2 + - - +
336A ASN* 1.3 55.5 + - - +
337A SER 3.1 2.9 - - - -
338A CYS* 2.7 36.7 + - + +
339A ILE* 3.0 19.1 + - + +
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Residues in contact with ASN 336 (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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121A ASP* 3.4 1.7 - - - +
158A ASN* 3.3 22.8 + - - +
159A MET* 5.5 3.4 - - - +
162A SER* 3.5 4.8 + - - -
295A MET* 3.9 23.1 - - + +
299A CYS* 3.3 21.3 - - + +
300A PHE* 4.3 10.1 - - + -
333A SER 2.5 26.5 + - - +
334A THR* 3.1 5.5 + - - +
335A LEU* 1.3 76.9 - - - +
337A SER* 1.3 60.0 + - - +
339A ILE* 3.1 3.6 + - - +
340A ASP* 2.7 38.6 + - - -
2202A NA 2.3 31.4 - - - -
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Residues in contact with SER 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 3.7 6.1 - - - +
89A ALA* 3.4 24.2 - - - +
93A ASN* 3.0 22.2 + - - -
121A ASP* 3.2 39.3 - - - -
125A VAL* 3.8 8.8 - - - +
128A PHE* 6.0 0.2 - - - -
158A ASN* 5.2 2.7 - - - -
334A THR 3.1 15.0 + - - -
336A ASN* 1.3 82.0 + - - +
338A CYS* 1.3 56.2 + - - +
340A ASP* 3.8 0.4 - - - -
341A PRO* 3.3 11.0 - - - +
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Residues in contact with CYS 338 (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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84A ILE* 5.1 2.9 - - - -
85A VAL* 3.7 44.0 - - - -
88A VAL* 3.8 31.1 - - + +
89A ALA* 4.1 4.0 - - - -
335A LEU* 2.7 19.3 + - + +
337A SER* 1.3 77.2 + - - +
339A ILE* 1.3 64.3 + - + +
340A ASP 3.4 0.4 - - - -
341A PRO* 3.3 14.1 - - - +
342A PHE* 3.6 17.3 - - - -
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Residues in contact with ILE 339 (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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291A THR* 3.6 32.8 - - + +
294A ALA* 5.5 5.4 - - + -
295A MET* 3.6 24.9 - - + +
298A ILE* 6.0 6.7 - - + -
299A CYS* 5.0 6.1 - - - -
335A LEU* 3.0 22.2 + - + +
336A ASN* 3.7 3.8 - - - +
338A CYS* 1.3 83.4 - - + +
340A ASP* 1.3 66.6 + - - +
341A PRO* 3.3 1.3 - - - -
342A PHE* 3.0 31.6 + - + +
343A VAL* 3.5 4.9 + - - +
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Residues in contact with ASP 340 (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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93A ASN* 4.1 0.4 - - - +
117A LEU* 3.4 27.5 - - - +
121A ASP* 2.7 23.5 - - - +
162A SER* 5.6 0.6 - - - -
166A LEU* 4.9 0.5 - - - +
295A MET* 3.5 19.4 - - - +
336A ASN* 2.7 19.1 + - - +
337A SER* 4.1 1.1 - - - -
339A ILE* 1.3 77.1 - - - +
341A PRO* 1.4 67.6 - - + +
343A VAL* 3.0 19.1 + - - +
344A TYR* 3.2 22.8 + - - +
2202A NA 2.5 30.1 - - - -
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Residues in contact with PRO 341 (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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88A VAL* 5.8 2.0 - - + -
92A SER* 3.5 35.0 - - - +
93A ASN* 4.5 6.5 - - - +
337A SER 3.3 17.7 - - - +
338A CYS* 3.3 17.0 - - - +
339A ILE 3.4 0.2 - - - -
340A ASP* 1.4 91.4 - - + +
342A PHE* 1.3 63.2 + - + +
344A TYR* 3.3 12.3 + - + -
345A TYR* 3.2 19.8 + - - +
351A PHE* 3.4 20.5 - - + -
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Residues in contact with PHE 342 (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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291A THR* 3.9 17.3 - - + +
338A CYS 3.6 19.5 - - - -
339A ILE* 3.0 28.7 + - + +
341A PRO* 1.3 80.2 - - + +
343A VAL* 1.3 63.0 + - - +
345A TYR* 3.4 9.1 + + + +
346A PHE* 3.2 42.8 + + + -
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Residues in contact with VAL 343 (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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117A LEU* 4.7 2.7 - - + -
166A LEU* 4.5 15.0 - - + -
169A LEU* 3.8 27.8 - - + -
288A LEU* 4.0 20.6 - - + -
291A THR* 3.8 21.8 - - + -
292A VAL* 4.8 4.5 - - + -
295A MET* 4.0 16.6 - - + -
339A ILE 3.8 7.6 - - - +
340A ASP* 3.0 13.6 + - - +
342A PHE* 1.3 75.3 - - - +
344A TYR* 1.3 70.6 + - + +
345A TYR 3.3 0.2 + - - -
346A PHE* 3.3 2.8 + - - +
347A VAL* 3.2 23.6 + - - +
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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
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93A ASN* 3.0 29.6 + - - -
96A ALA* 3.6 27.1 - - + -
100A PHE* 3.9 12.6 - + + -
114A MET* 3.9 38.4 - - + -
117A LEU* 3.5 23.9 - - + +
118A ALA* 3.1 19.5 + - + -
121A ASP* 3.2 7.3 + - - -
340A ASP* 3.2 25.1 + - + +
341A PRO* 3.3 11.8 + - + +
343A VAL* 1.3 78.6 - - + +
345A TYR* 1.3 59.3 + - - +
348A SER* 2.8 34.5 + - - +
351A PHE* 3.5 18.5 - + + -
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Residues in contact with TYR 345 (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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341A PRO 3.2 12.7 + - - +
342A PHE* 3.6 15.3 - + + +
343A VAL 3.1 0.6 - - - -
344A TYR* 1.3 78.6 - - - +
346A PHE* 1.3 80.7 + + - +
351A PHE* 3.5 8.9 - + + -
352A ARG* 2.7 68.8 + - + +
355A ALA* 4.1 22.4 - - + -
356A LYS* 3.3 29.3 + - + +
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Residues in contact with PHE 346 (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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173A ARG* 4.8 8.0 + - - -
284A ARG* 3.9 34.7 - - + +
287A LYS* 3.7 34.5 - - + -
288A LEU* 3.8 25.6 - - + +
291A THR* 3.2 25.8 - - - -
342A PHE* 3.2 31.4 + + + +
343A VAL 3.3 4.7 + - - +
344A TYR 3.3 0.4 - - - -
345A TYR* 1.3 104.9 - + - +
347A VAL* 1.3 62.5 + - - +
352A ARG* 3.6 14.6 + - - +
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Residues in contact with VAL 347 (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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110A ALA* 4.2 6.1 - - + -
114A MET* 3.6 25.1 - - + -
169A LEU* 4.1 19.5 - - + -
173A ARG* 3.6 37.6 + - - +
288A LEU* 3.8 27.1 - - + -
343A VAL 3.2 17.1 + - - +
346A PHE* 1.3 83.2 - - - +
348A SER* 1.3 65.2 + - - +
349A HIS* 3.5 22.5 + - - -
352A ARG* 4.2 1.7 + - - -
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Residues in contact with SER 348 (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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100A PHE* 3.6 13.1 - - - -
104A THR* 4.6 1.7 + - - +
111A VAL* 5.5 4.2 - - - +
114A MET* 3.7 22.0 - - - -
344A TYR 2.8 22.4 + - - +
345A TYR 3.7 1.2 - - - +
347A VAL* 1.3 74.9 - - - +
349A HIS* 1.3 60.6 + - - +
350A ASP* 3.5 8.1 + - - +
351A PHE* 3.1 26.5 + - - +
352A ARG* 3.3 24.6 + - - +
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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
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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