Contacts of the helix formed by residues 28 - 42 (chain k) in PDB entry 5GAG
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 LYS 28 (chain k).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1535A A 3.5 33.7 + - + +
27k MET* 1.3 106.4 - - + +
29k GLN* 1.3 58.7 + - - +
31k THR* 4.0 1.3 - - - -
32k LEU* 3.0 42.1 + - + +
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Residues in contact with GLN 29 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427i MET* 4.6 8.9 - - - -
430i MET* 3.3 48.6 - - - +
27k MET* 4.8 0.8 - - - +
28k LYS* 1.3 75.7 - - - +
30k SER* 1.3 59.9 + - - +
32k LEU* 4.3 7.8 - - - +
33k ALA* 2.9 33.4 + - + +
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Residues in contact with SER 30 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27k MET* 3.3 25.7 + - - +
28k LYS 3.4 0.4 - - - -
29k GLN* 1.3 77.8 - - - +
31k THR* 1.3 57.3 + - - +
33k ALA* 3.8 2.9 - - - +
34k LEU* 2.9 44.4 + - - +
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Residues in contact with THR 31 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27k MET 2.4 31.8 + - - -
28k LYS* 4.3 1.8 - - - -
30k SER* 1.3 75.9 - - - +
32k LEU* 1.3 59.7 + - - +
34k LEU* 4.5 6.5 - - + +
35k LEU* 2.9 43.1 + - + +
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Residues in contact with LEU 32 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430i MET* 3.9 22.6 - - - +
28k LYS* 3.0 34.2 + - + +
29k GLN* 4.3 12.6 - - - +
31k THR* 1.3 73.0 - - - +
33k ALA* 1.3 66.4 + - - +
35k LEU* 5.0 2.7 - - + -
36k LEU* 3.0 48.2 + - + +
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Residues in contact with ALA 33 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337i GLN* 4.6 9.9 - - + +
427i MET* 4.3 15.9 - - + +
430i MET* 4.5 2.3 - - - +
29k GLN* 2.9 27.5 + - + +
30k SER* 3.8 4.5 - - - +
32k LEU* 1.3 79.7 - - - +
34k LEU* 1.3 66.1 + - + +
36k LEU* 3.8 0.3 - - - +
37k LEU* 2.9 40.4 + - + +
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Residues in contact with LEU 34 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341i MET* 3.8 28.9 - - + +
344i MET* 4.1 26.5 - - + -
30k SER* 2.9 36.8 + - - +
31k THR* 4.2 5.6 - - + +
33k ALA* 1.3 73.8 - - + +
35k LEU* 1.3 62.2 + - - +
37k LEU* 3.7 6.2 - - + +
38k LEU* 3.0 35.8 + - + +
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Residues in contact with LEU 35 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31k THR* 2.9 31.4 + - + +
32k LEU* 5.0 2.7 - - + -
34k LEU* 1.3 72.1 - - - +
36k LEU* 1.3 75.8 + - + +
37k LEU 3.0 0.5 + - - -
38k LEU* 4.4 0.6 - - - +
39k LEU* 2.9 65.2 + - + +
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Residues in contact with LEU 36 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423i MET* 4.1 5.1 - - - +
426i MET* 4.6 21.5 - - + -
427i MET* 5.4 2.9 - - + -
430i MET* 3.8 25.1 - - + -
32k LEU* 3.0 34.5 - - + +
33k ALA 3.4 1.4 + - - +
35k LEU* 1.3 93.4 - - + +
37k LEU* 1.3 57.7 + - - +
39k LEU* 4.4 2.9 - - + -
40k LEU* 2.9 39.5 + - + +
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Residues in contact with LEU 37 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334i PHE* 4.9 2.9 - - + -
337i GLN* 3.3 41.7 - - + +
341i MET* 3.7 25.8 - - + -
423i MET* 3.6 34.7 - - + +
427i MET* 3.8 19.7 - - + -
33k ALA* 2.9 35.4 + - + +
34k LEU* 3.7 5.8 - - + +
35k LEU 3.0 1.2 + - - -
36k LEU* 1.3 73.1 - - - +
38k LEU* 1.3 66.2 + - - +
41k LEU* 2.9 32.6 + - + +
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Residues in contact with LEU 38 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341i MET* 4.8 15.3 - - + +
345i GLY* 4.8 9.9 - - - -
346i GLY 4.2 17.0 - - - +
369i ASP* 3.2 35.0 - - - +
373i LEU* 5.6 3.4 - - + -
34k LEU* 3.0 24.1 + - + +
35k LEU* 4.4 0.4 - - - +
37k LEU* 1.3 75.7 - - - +
39k LEU* 1.3 68.5 + - + +
41k LEU* 3.2 15.6 - - + +
42k THR* 3.1 21.9 + - - +
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Residues in contact with LEU 39 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35k LEU* 2.9 61.0 + - + +
36k LEU* 4.4 2.9 - - + -
38k LEU* 1.3 73.0 - - + +
40k LEU* 1.3 51.2 + - - +
42k THR* 2.5 36.2 + - + +
43k PRO* 2.8 12.3 - - - +
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Residues in contact with LEU 40 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422i ASP* 5.8 3.1 - - + +
423i MET* 3.6 22.9 - - + +
426i MET* 3.7 33.4 - - + -
36k LEU* 2.9 28.0 + - + +
39k LEU* 1.3 71.8 - - - +
41k LEU* 1.3 60.0 + - - +
42k THR 3.3 0.2 - - - -
43k PRO* 3.5 23.7 - - + +
44k VAL* 3.7 30.4 - - + +
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Residues in contact with LEU 41 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50V PRO* 6.0 0.2 - - - +
334i PHE* 5.2 3.4 - - + -
338i LEU* 5.7 0.7 - - + -
341i MET* 4.4 16.8 - - + -
372i VAL* 6.1 2.9 - - + -
373i LEU* 6.1 1.1 - - + -
376i MET* 4.0 26.9 - - + -
419i GLN* 3.7 45.3 + - + +
423i MET* 4.1 18.1 - - + +
37k LEU* 2.9 31.1 + - + +
38k LEU* 3.2 16.4 - - + +
39k LEU 2.9 0.2 + - - -
40k LEU* 1.3 77.5 - - - +
42k THR* 1.3 63.8 + - - +
44k VAL* 4.7 4.7 + - - +
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Residues in contact with THR 42 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50V PRO* 3.8 20.2 - - - +
53V ASN* 6.1 1.3 - - - +
38k LEU* 3.1 13.4 + - - +
39k LEU* 2.5 27.6 + - + +
41k LEU* 1.3 73.1 - - - +
43k PRO* 1.4 71.3 - - + +
44k VAL 3.5 0.5 + - - -
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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