Contacts of the helix formed by residues 25 - 36 (chain D) in PDB entry 3SF4
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 VAL 25 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A LEU* 6.4 1.1 - - + -
24D GLN* 1.3 77.7 - - - +
26D ASP* 1.3 69.5 + - - +
27D SER 3.4 2.7 - - - -
28D VAL* 3.0 11.6 + - + -
29D GLN* 2.7 33.9 + - + +
23E MET* 3.4 36.1 - - + +
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Residues in contact with ASP 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A TRP* 3.0 30.0 + - + -
323A ASN* 2.8 25.3 + - - +
356A THR* 4.9 8.0 - - - +
360A ASN* 4.8 6.4 + - - -
24D GLN* 4.5 1.4 - - - +
25D VAL* 1.3 81.7 - - - +
27D SER* 1.3 78.4 + - - -
29D GLN* 3.2 8.0 + - - +
30D ARG* 3.1 21.1 + - - +
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Residues in contact with SER 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A TYR* 4.9 2.2 + - - -
283A ASN* 4.0 2.7 + - - +
316A ARG* 4.3 4.3 + - - -
319A TRP* 3.7 30.7 - - - -
320A SER* 3.9 23.8 + - - -
323A ASN* 2.7 30.4 + - - +
24D GLN 4.3 1.2 + - - -
26D ASP* 1.3 81.1 + - - +
28D VAL* 1.3 71.0 + - - +
30D ARG* 3.4 4.2 + - - +
31D TRP* 3.1 20.8 + - - +
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Residues in contact with VAL 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ASN* 3.3 23.1 - - - +
286A THR* 3.7 31.6 - - + -
287A LEU* 4.0 33.2 - - + -
298A HIS* 6.3 0.2 - - - +
24D GLN 4.2 8.5 - - - +
25D VAL* 3.0 11.8 + - + +
27D SER* 1.3 81.9 + - - +
29D GLN* 1.3 60.4 + - - +
31D TRP* 3.1 10.9 + - + +
32D MET* 2.9 33.0 + - + +
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Residues in contact with GLN 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D VAL* 2.7 27.6 + - + +
26D ASP* 3.3 8.7 - - - +
28D VAL* 1.3 78.0 - - - +
30D ARG* 1.3 57.1 + - - +
32D MET* 3.3 16.3 + - - +
33D GLU* 3.0 55.1 + - - +
36D LYS* 5.9 2.0 - - - +
23E MET* 6.1 0.9 - - - +
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Residues in contact with ARG 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A ARG* 3.2 28.3 - - - +
319A TRP* 3.9 28.3 - - + -
350A ASP* 5.6 4.4 + - - -
352A SER* 4.5 17.2 + - - -
26D ASP 3.1 9.1 + - - +
27D SER 3.7 7.6 - - - +
28D VAL 3.3 0.2 - - - -
29D GLN* 1.3 79.8 - - - +
31D TRP* 1.3 62.0 + - - +
33D GLU* 3.5 19.4 + - - +
34D ASP* 3.3 35.1 + - - +
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Residues in contact with TRP 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ILE* 3.7 26.7 - - + -
258A TYR* 4.0 2.2 - - - -
279A TYR* 3.8 16.3 - + + -
280A SER* 3.5 42.2 + - - +
283A ASN* 3.4 48.9 - - + +
284A THR* 4.0 5.8 - - - -
287A LEU* 4.2 10.5 - - + -
316A ARG* 4.0 9.9 - - - +
27D SER 3.1 9.5 + - - +
28D VAL* 3.1 11.6 + - + +
30D ARG* 1.3 76.6 - - - +
32D MET* 1.3 84.4 + - + +
34D ASP* 3.3 6.4 + - + +
35D LEU* 2.9 63.3 + - + +
38D MET* 6.1 1.3 - - + +
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Residues in contact with MET 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ILE* 3.4 28.0 - - + +
247A PHE* 3.4 21.1 - - + -
287A LEU* 4.2 15.5 - - + -
28D VAL* 2.9 30.6 + - + +
29D GLN* 3.3 15.2 + - - +
31D TRP* 1.3 88.9 - - + +
33D GLU* 1.3 57.9 + - - +
35D LEU* 4.0 7.2 - - - -
36D LYS* 2.9 30.4 + - - +
19E PRO* 3.1 41.7 - - + +
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Residues in contact with GLU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLN* 3.0 49.3 + - - +
30D ARG* 3.6 24.4 + - - +
31D TRP 3.3 0.2 - - - -
32D MET* 1.3 78.9 - - - +
34D ASP* 1.3 64.5 + - - +
36D LYS* 3.6 31.8 - - - +
37D LEU* 4.2 10.0 + - - +
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Residues in contact with ASP 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A ARG* 3.7 22.9 + - - -
30D ARG* 3.3 26.3 + - - +
31D TRP* 3.8 6.6 - - + +
32D MET 3.2 0.2 - - - -
33D GLU* 1.3 74.4 - - - +
35D LEU* 1.3 69.5 + - - +
36D LYS 3.0 1.8 - - - -
37D LEU* 2.8 21.1 + - - +
38D MET* 3.3 17.5 + - + +
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Residues in contact with LEU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A TYR* 2.7 24.7 + - - +
243A ASN* 3.2 32.7 + - - +
246A ILE* 4.1 11.7 - - + -
247A PHE* 4.0 15.7 - - + -
258A TYR* 3.6 11.2 - - - +
280A SER* 4.6 5.2 - - - +
31D TRP* 2.9 60.4 + - + +
32D MET* 3.6 6.3 - - - +
34D ASP* 1.3 75.9 - - - +
36D LYS* 1.3 58.4 + - - +
38D MET* 3.1 35.5 + - + +
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Residues in contact with LYS 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A TYR* 3.6 18.6 - - - +
207A LEU* 3.9 9.7 - - - +
211A PHE* 6.5 0.9 - - + -
247A PHE* 3.8 28.6 - - + -
248B LEU 5.8 3.6 - - - +
29D GLN* 5.9 2.0 - - - +
32D MET* 2.9 14.2 + - - +
33D GLU* 3.6 32.6 - - - +
34D ASP 2.9 0.2 + - - -
35D LEU* 1.3 76.9 - - - +
37D LEU* 1.3 64.6 + - + +
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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