Contacts of the helix formed by residues 33 - 49 (chain Y) in PDB entry 6CP3
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 ILE 33 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24Y TYR* 4.8 18.6 - - + +
27Y ALA* 3.9 23.1 - - + +
28Y ALA* 4.4 7.6 - - + +
31Y SER 2.6 19.9 + - - +
32Y SER* 1.3 72.9 - - - +
34Y ASP* 1.3 72.1 + - + +
35Y ALA 3.2 1.3 - - - -
36Y ALA* 3.1 6.5 + - - +
37Y PHE* 2.6 37.3 + - - +
108Y PHE* 4.2 13.1 - - + -
112Y ASN* 4.2 17.5 - - - +
115Y HIS* 4.0 27.1 - - + +
116Y ASN* 5.8 0.7 - - - +
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Residues in contact with ASP 34 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Y ILE* 1.3 85.8 - - + +
35Y ALA* 1.3 56.7 + - - +
37Y PHE* 3.1 10.9 + - + +
38Y GLN* 2.6 38.3 + - - +
112Y ASN* 5.4 2.5 - - - +
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Residues in contact with ALA 35 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Y SER* 4.6 17.5 - - - +
33Y ILE 3.2 0.8 - - - +
34Y ASP* 1.3 78.3 - - - +
36Y ALA* 1.3 54.2 + - - +
38Y GLN* 3.1 6.5 + - - +
39Y SER* 2.7 38.1 + - - -
82Y ASP* 4.7 9.1 - - + +
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Residues in contact with ALA 36 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Y LEU* 5.9 3.6 - - + -
27Y ALA* 5.2 7.0 - - + -
32Y SER 3.6 16.0 + - - +
33Y ILE* 3.1 11.5 + - - +
35Y ALA* 1.3 78.6 - - - +
37Y PHE* 1.3 58.3 + - - +
39Y SER* 2.5 23.5 + - - -
40Y LEU* 2.8 21.6 + - - +
82Y ASP* 4.7 6.2 - - + +
84Y TYR* 6.0 3.8 - - + -
85Y VAL* 4.5 15.5 - - + -
108Y PHE* 4.5 11.0 - - + -
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Residues in contact with PHE 37 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Y ILE 2.6 20.7 + - - +
34Y ASP* 3.4 8.3 - - - +
36Y ALA* 1.3 73.4 - - - +
38Y GLN* 1.3 63.1 + - + +
40Y LEU* 3.2 5.8 + - + +
41Y GLN* 2.9 60.3 + - + +
108Y PHE* 3.8 23.3 - + + -
109Y GLY* 3.5 28.7 - - - -
112Y ASN* 2.7 38.1 - - + +
113Y ASP* 5.7 2.9 - - + -
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Residues in contact with GLN 38 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Y ASP 2.6 19.9 + - - +
35Y ALA* 3.5 8.5 - - - +
37Y PHE* 1.3 76.2 - - + +
39Y SER* 1.3 61.9 + - - +
41Y GLN* 3.0 23.1 + - - +
42Y LYS* 2.8 37.1 + - + +
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Residues in contact with SER 39 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Y ALA 2.7 17.5 + - - -
36Y ALA* 2.5 26.9 + - - -
38Y GLN* 1.3 72.2 - - - +
40Y LEU* 1.3 57.1 + - - +
42Y LYS* 3.3 8.6 + - - +
43Y VAL* 2.9 31.0 + - - +
78Y HIS* 5.6 5.0 - - - -
81Y LEU* 5.1 3.4 - - - -
82Y ASP* 3.6 20.3 - - - +
85Y VAL* 3.4 18.9 - - - +
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Residues in contact with LEU 40 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Y LEU* 4.5 10.8 - - + -
36Y ALA 2.8 16.0 + - - +
37Y PHE* 3.4 8.1 - - + +
38Y GLN 3.2 0.2 - - - -
39Y SER* 1.3 74.8 + - - +
41Y GLN* 1.3 61.6 + - + +
43Y VAL* 3.3 13.7 - - + +
44Y GLU* 2.9 31.8 + - - +
85Y VAL* 3.8 26.2 - - + -
101Y PHE* 5.3 11.4 - - + -
104Y ILE* 6.0 0.9 - - + -
105Y ALA* 5.1 20.3 - - + +
108Y PHE* 2.9 52.0 - - + -
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Residues in contact with GLN 41 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Y PHE* 2.9 52.7 + - + +
38Y GLN* 3.0 27.6 + - - +
40Y LEU* 1.3 78.0 - - - +
42Y LYS* 1.3 56.5 + - - +
44Y GLU* 3.8 6.8 - - - +
45Y SER* 2.9 31.1 + - - -
105Y ALA 5.6 2.6 + - - -
109Y GLY* 5.4 2.4 - - - -
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Residues in contact with LYS 42 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Y GLN* 2.8 27.3 + - + +
39Y SER* 3.7 9.0 - - - +
40Y LEU 3.2 0.2 - - - -
41Y GLN* 1.3 74.3 - - - +
43Y VAL* 1.3 57.0 + - - +
45Y SER* 3.4 8.6 + - - -
46Y THR* 2.9 34.0 + - + +
78Y HIS* 5.2 14.7 - - + +
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Residues in contact with VAL 43 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39Y SER 2.9 17.3 + - - +
40Y LEU* 3.3 22.4 - - + +
42Y LYS* 1.3 73.7 - - - +
44Y GLU* 1.3 63.0 + - + +
46Y THR* 3.3 10.4 - - + +
47Y VAL* 2.9 32.9 + - + +
74Y ILE* 4.1 34.3 - - + -
78Y HIS* 5.2 12.0 - - + -
85Y VAL* 6.1 2.2 - - + -
89Y LEU* 5.3 6.5 - - + -
101Y PHE* 4.3 24.9 - - + -
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Residues in contact with GLU 44 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40Y LEU 2.9 19.7 + - - +
41Y GLN* 3.8 7.4 - - - +
43Y VAL* 1.3 79.1 - - + +
45Y SER* 1.3 57.0 + - - +
47Y VAL* 3.4 12.8 + - - +
48Y LYS* 2.9 30.3 + - + +
101Y PHE* 5.0 7.8 - - - -
102Y GLU* 3.2 40.3 - - - +
105Y ALA* 3.9 14.6 - - + +
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Residues in contact with SER 45 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Y GLN 2.9 19.2 + - - -
42Y LYS* 3.8 9.6 - - - -
44Y GLU* 1.3 78.7 - - - +
46Y THR* 1.3 51.8 + - - +
48Y LYS* 3.0 7.0 + - - +
49Y LYS* 2.6 40.6 + - - +
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Residues in contact with THR 46 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42Y LYS* 2.9 22.9 + - + +
43Y VAL* 3.3 23.8 - - + +
45Y SER* 1.3 73.6 - - - +
47Y VAL* 1.3 68.7 + - + +
49Y LYS* 4.0 6.8 - - - +
50Y ASN* 3.6 19.9 + - - +
74Y ILE* 5.6 7.6 - - + +
77Y THR* 4.8 18.1 + - + +
78Y HIS* 6.0 3.8 - - + -
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Residues in contact with VAL 47 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43Y VAL* 2.9 25.4 + - + +
44Y GLU* 3.6 15.5 - - - +
46Y THR* 1.3 79.1 - - + +
48Y LYS* 1.3 62.7 + - - +
50Y ASN 3.2 22.3 + - - +
51Y PRO* 4.0 3.1 - - - +
54Y GLY* 3.4 32.3 - - - +
55Y HIS* 4.3 6.6 + - + +
58Y LEU* 4.8 10.5 - - + -
74Y ILE* 4.8 18.6 - - + -
101Y PHE* 5.0 13.0 - - + -
102Y GLU* 6.5 0.7 - - + -
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Residues in contact with LYS 48 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Y GLU* 2.9 23.0 + - + +
45Y SER* 3.0 7.8 + - - +
47Y VAL* 1.3 78.3 - - - +
49Y LYS* 1.3 57.0 + - - +
50Y ASN 3.1 4.7 + - - -
51Y PRO* 3.9 16.7 - - - +
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Residues in contact with LYS 49 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Y SER* 2.6 24.4 + - - +
46Y THR* 4.2 6.1 - - - -
47Y VAL 3.3 0.4 - - - -
48Y LYS* 1.3 72.1 - - - +
50Y ASN* 1.3 58.6 + - - +
51Y PRO* 3.9 5.6 - - - +
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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