Contacts of the helix formed by residues 440 - 447 (chain A) in PDB entry 3F4V
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 GLU 440 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLN* 3.1 20.8 + - - +
356A SER* 5.4 1.8 - - - +
358A TRP* 5.2 2.3 - - - -
433A TRP* 3.9 8.3 + - - -
438A ASN* 3.3 4.8 + - - +
439A PHE* 1.3 69.0 - - - +
441A TRP* 1.3 77.9 + - - +
442A LEU 3.2 0.9 + - - -
443A SER* 2.9 17.3 + - - +
444A GLY 2.8 19.7 + - - +
447A SER* 3.5 37.9 - - - +
449A PHE* 3.8 19.9 - - + -
1004A GOL 2.8 29.6 + - - -
1005A GOL 4.4 8.8 + - - -
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Residues in contact with TRP 441 (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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26A SER* 4.2 2.2 - - - -
28A TYR* 3.9 22.7 - + + -
29A GLN* 3.2 35.1 - - + +
44A TRP* 3.4 60.8 - + + -
54A VAL* 3.5 11.4 - - - +
130A HIS* 3.8 23.1 - + - -
131A TYR* 3.4 34.6 - + + -
132A ASP* 6.0 0.4 - - + -
190A ASN* 5.4 2.7 - - - +
439A PHE* 3.2 20.9 + + - -
440A GLU* 1.3 82.2 - - - +
442A LEU* 1.3 68.2 + - + +
444A GLY 2.9 10.2 + - - -
1004A GOL 3.0 34.5 + - - -
1005A GOL 4.8 4.0 - - - -
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Residues in contact with LEU 442 (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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44A TRP* 4.2 1.8 - - + -
47A PHE* 3.5 24.9 - - + -
53A ASN 3.5 14.9 - - - +
54A VAL* 3.8 2.7 - - - +
55A ALA* 2.9 28.3 + - - +
183A LEU* 5.6 3.1 - - + -
189A THR* 3.4 39.7 - - - +
190A ASN* 3.8 15.9 - - - +
440A GLU 3.2 0.6 + - - -
441A TRP* 1.3 80.5 - - + +
443A SER* 1.3 58.0 + - - +
444A GLY 3.2 0.4 - - - -
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Residues in contact with SER 443 (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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55A ALA* 3.4 10.0 - - - +
355A ASN* 5.4 2.4 + - - -
356A SER* 5.0 5.2 + - - -
440A GLU* 2.9 14.3 + - - +
442A LEU* 1.3 78.0 - - - +
444A GLY* 1.3 64.3 + - - +
445A TYR 3.2 0.3 + - - -
446A THR* 2.6 36.3 + - - -
447A SER* 3.8 22.3 - - - -
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Residues in contact with GLY 444 (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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54A VAL* 3.7 16.1 - - - +
55A ALA 4.7 3.6 - - - -
58A GLN* 4.8 0.4 - - - -
438A ASN 3.7 1.7 - - - +
439A PHE* 3.8 13.9 - - - -
440A GLU* 2.8 30.4 + - - +
441A TRP 2.9 15.7 + - - -
442A LEU 3.2 1.8 + - - -
443A SER* 1.3 77.7 - - - +
445A TYR* 1.3 63.4 + - - -
446A THR 3.4 1.6 + - - -
447A SER 4.1 1.0 + - - -
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Residues in contact with TYR 445 (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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55A ALA 5.3 0.2 + - - -
58A GLN* 3.7 35.1 - - + +
59A ASN 2.8 29.2 + - - -
63A ALA* 3.1 27.6 + - - +
393A ALA* 4.9 0.9 - - - +
438A ASN 3.7 9.6 - - - -
439A PHE* 3.7 33.4 - + + +
443A SER 3.2 0.4 + - - -
444A GLY* 1.3 70.0 - - - -
446A THR* 1.3 62.7 + - - +
447A SER 3.3 3.6 - - - -
448A LYS* 2.9 35.9 + - - +
456A PHE* 3.6 50.9 - + + -
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Residues in contact with THR 446 (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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55A ALA* 3.9 19.3 - - + +
56A GLY* 5.7 0.4 - - - +
355A ASN* 3.6 11.7 + - - +
392A PRO* 3.6 0.7 - - - +
393A ALA* 3.2 41.8 + - + -
443A SER* 2.6 31.0 + - - +
445A TYR* 1.3 81.6 - - - +
447A SER* 1.3 56.9 + - - +
448A LYS* 4.2 1.8 - - - -
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Residues in contact with SER 447 (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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355A ASN* 3.8 5.2 - - - +
356A SER* 4.7 0.9 - - - -
390A ASP* 2.7 25.1 + - - -
391A GLN 3.8 3.6 - - - -
438A ASN 3.9 18.4 + - - +
440A GLU* 3.5 23.3 - - - +
443A SER* 3.8 14.3 + - - -
444A GLY 4.1 1.1 + - - +
445A TYR 3.3 1.4 - - - -
446A THR* 1.3 79.3 + - - +
448A LYS* 1.3 64.1 + - - +
449A PHE* 3.2 22.3 + - - -
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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