Contacts of the helix formed by residues 337 - 344 (chain A) in PDB entry 3W5D
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 PRO 337 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A THR* 3.3 21.1 + - + +
250A GLN* 3.4 28.9 - - + +
319A LEU* 4.6 8.3 - - + -
335A SER* 3.2 14.1 - - - +
336A LEU* 1.4 93.7 - - + +
338A SER* 1.3 57.9 + - - -
339A VAL 3.3 0.6 + - - -
340A GLU* 3.6 13.1 + - + +
341A THR* 3.3 14.4 + - - -
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Residues in contact with SER 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A THR* 5.1 0.9 - - - -
333A VAL* 4.2 9.9 - - - -
335A SER* 2.8 35.3 + - - -
337A PRO* 1.3 76.0 - - - +
339A VAL* 1.3 54.0 + - - +
340A GLU 3.1 3.1 - - - -
341A THR* 3.1 10.5 + - - -
342A LEU* 2.8 37.7 + - - +
715A GLU 5.7 0.4 - - - -
716A ILE* 5.0 2.8 - - - +
732A GLU* 3.3 34.4 - - - +
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Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 4.5 15.7 - - + +
323A THR* 3.9 13.9 - - - +
326A MET* 3.5 31.6 - - + -
333A VAL* 4.0 9.9 - - + -
336A LEU* 3.2 18.1 + - - +
338A SER* 1.3 76.7 - - - +
340A GLU* 1.3 60.9 + - - +
342A LEU* 3.8 7.7 - - - +
343A GLY 3.7 3.3 + - - -
750A GLY* 3.5 22.5 - - - +
753A ILE* 3.7 42.4 - - + -
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Residues in contact with GLU 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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247A THR* 2.9 26.9 + - - -
248A PRO* 3.0 35.6 - - - +
249A LEU* 3.0 27.3 + - + +
319A LEU* 5.7 1.8 - - + +
336A LEU 4.6 0.4 + - - -
337A PRO* 3.6 8.5 + - + +
338A SER 3.1 0.4 - - - -
339A VAL* 1.3 77.1 - - - +
341A THR* 1.3 66.4 + - - +
343A GLY* 3.1 12.8 + - - -
344A CYS* 3.5 11.4 + - - -
750A GLY 4.9 4.7 - - - +
753A ILE* 6.5 0.2 - - - -
754A TYR* 3.9 27.0 - - + +
757A MET* 4.0 19.0 - - + +
822A ARG* 3.3 11.3 + - - +
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Residues in contact with THR 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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247A THR* 3.3 21.9 - - + +
248A PRO* 4.3 11.4 - - + +
337A PRO 3.3 14.2 + - - -
338A SER* 3.1 9.8 + - - -
340A GLU* 1.3 79.8 - - - +
342A LEU* 1.3 63.2 + - - +
344A CYS* 2.9 20.8 + - + +
345A THR 3.2 8.0 + - - -
697A ILE* 3.7 24.4 - - + +
715A GLU* 3.9 19.1 - - + +
716A ILE* 3.9 12.8 - - + -
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Residues in contact with LEU 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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326A MET* 4.6 5.6 - - - -
333A VAL* 4.5 13.5 - - + -
338A SER* 2.8 18.0 + - - +
339A VAL* 3.8 10.1 - - - +
340A GLU 3.2 0.2 - - - -
341A THR* 1.3 76.7 - - - +
343A GLY* 1.3 62.3 + - - +
345A THR* 2.7 26.6 + - + +
716A ILE* 4.0 26.2 - - + -
718A ILE* 5.7 0.2 - - + -
733A MET* 3.9 22.9 - - + -
743A ILE* 5.4 2.0 - - + -
746A ALA* 3.5 38.4 - - + +
747A VAL* 3.2 31.5 - - + +
750A GLY* 5.7 0.2 - - - -
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Residues in contact with GLY 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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339A VAL 3.7 3.6 + - - -
340A GLU 3.1 9.9 + - - -
342A LEU* 1.3 79.7 - - - +
344A CYS* 1.3 58.5 + - - +
345A THR 3.7 0.5 + - - +
747A VAL* 3.8 7.8 - - - +
750A GLY* 3.8 3.7 - - - -
751A ARG* 3.3 55.2 + - - +
754A TYR* 6.1 0.9 - - - -
822A ARG* 5.0 4.7 + - - +
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Residues in contact with CYS 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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248A PRO* 4.5 5.4 - - - -
340A GLU* 3.5 16.2 - - - -
341A THR* 2.9 11.8 + - - +
343A GLY* 1.3 76.5 - - - +
345A THR* 1.3 68.1 + - - +
346A SER* 2.9 5.2 + - - -
697A ILE* 3.5 23.5 - - + +
821A PRO* 3.7 12.4 - - - +
822A ARG* 3.3 65.4 - - - +
824A PRO* 5.4 1.8 - - + -
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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