Contacts of the helix formed by residues 30 - 49 (chain K) in PDB entry 6MZL
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 HIS 30 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470G TYR* 3.1 19.3 + - + +
471G GLN* 4.9 6.1 - - - +
28K ASN 4.4 3.3 - - - +
29K TYR* 1.3 79.9 - - - +
31K LEU* 1.3 67.5 + - - +
32K ALA 3.1 2.1 + - - -
33K ARG* 3.3 35.6 + - - +
34K ARG* 4.1 10.6 + - + +
66K GLN* 5.5 1.1 - - - -
137O TYR* 3.1 38.2 + - - -
138O TYR* 3.8 20.5 + + - -
141O ARG* 4.7 9.6 + - - -
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Residues in contact with LEU 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K ASN* 3.2 19.3 + - - +
30K HIS* 1.3 83.5 - - - +
32K ALA* 1.3 57.6 + - - +
34K ARG* 3.0 57.6 + - - +
35K ARG* 3.0 37.5 + - - +
34M ARG* 4.7 14.6 - - - +
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Residues in contact with ALA 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K TYR 4.2 8.2 + - - +
30K HIS 3.1 1.6 + - - -
31K LEU* 1.3 78.6 - - - +
33K ARG* 1.3 53.5 + - + +
35K ARG* 3.4 9.6 + - - +
36K THR* 2.5 38.5 + - - +
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Residues in contact with ARG 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470G TYR* 5.0 3.4 + - - -
471G GLN* 5.1 3.6 - - - +
29K TYR 5.0 3.4 + - - -
30K HIS* 3.3 35.2 + - - +
31K LEU 3.2 0.8 - - - -
32K ALA* 1.3 76.9 - - + +
34K ARG* 1.3 59.4 + - - +
36K THR* 3.2 9.1 + - - +
37K LEU* 2.9 32.6 + - - +
134O VAL* 4.0 30.7 - - + +
137O TYR* 3.2 62.6 + - - +
138O TYR* 4.3 8.3 - - + +
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Residues in contact with ARG 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K HIS* 4.1 9.8 + - + -
31K LEU* 3.0 43.6 + - - +
33K ARG* 1.3 80.3 - - - +
35K ARG* 1.3 62.0 + - - +
37K LEU* 3.1 9.4 + - + +
38K GLN* 3.0 56.4 + - - +
59K GLU* 4.6 17.2 + - - +
62K THR* 4.1 8.9 - - + +
63K GLU* 3.3 30.2 + - - +
66K GLN* 4.5 15.3 - - - +
34M ARG* 4.5 12.3 - - - +
138O TYR* 4.0 12.2 + - - +
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Residues in contact with ARG 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K LEU* 3.0 38.9 + - + +
32K ALA* 3.9 9.4 - - - +
33K ARG 3.3 0.2 - - - -
34K ARG* 1.3 79.4 - - - +
36K THR* 1.3 59.1 + - - +
38K GLN* 3.2 30.7 + - - +
39K VAL* 2.9 31.4 + - - +
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Residues in contact with THR 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K ALA* 2.5 22.1 + - - +
33K ARG* 3.3 13.8 - - - -
35K ARG* 1.3 74.3 - - - +
37K LEU* 1.3 63.9 + - + +
39K VAL* 3.1 13.8 + - + +
40K VAL* 3.0 23.1 + - + +
131O PRO* 3.9 30.3 - - + -
134O VAL* 4.5 13.4 - - + +
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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
----------------------------------------------------------
33K ARG 2.9 15.5 + - - +
34K ARG* 3.3 9.0 - - + +
36K THR* 1.3 78.1 - - + +
38K GLN* 1.3 57.3 + - - +
40K VAL* 3.1 10.5 + - + +
41K VAL* 2.9 30.8 + - - +
62K THR* 3.7 16.2 - - + +
65K LEU* 5.3 10.3 - - + +
66K GLN* 4.0 23.3 - - + +
69K ILE* 5.0 13.7 - - + -
130O ILE* 4.9 16.6 - - + -
131O PRO* 6.3 0.2 - - + -
134O VAL* 4.1 18.4 - - + -
135O THR* 6.4 0.7 - - - -
138O TYR* 3.6 35.9 - - + +
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Residues in contact with GLN 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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34K ARG* 3.0 51.4 + - - +
35K ARG* 3.2 31.9 + - - +
37K LEU* 1.3 77.2 - - - +
39K VAL* 1.3 55.4 + - + +
41K VAL* 3.2 10.5 + - - +
42K SER* 2.9 27.2 + - - -
58K VAL* 5.6 5.0 - - + +
59K GLU* 3.5 32.2 + - + +
62K THR* 4.0 18.4 - - + +
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Residues in contact with VAL 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K ARG 2.9 19.2 + - - +
36K THR* 3.1 15.0 + - + +
38K GLN* 1.3 73.9 - - - +
40K VAL* 1.3 62.6 + - + +
42K SER* 3.2 7.8 + - - +
43K SER* 2.9 37.5 + - - +
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Residues in contact with VAL 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K THR* 3.0 15.1 + - + +
37K LEU* 3.1 15.2 + - + +
39K VAL* 1.3 77.3 - - + +
41K VAL* 1.3 58.7 + - - +
43K SER* 3.2 7.9 + - - -
44K LEU* 3.0 44.8 + - + +
65K LEU* 5.4 9.4 - - + -
129O THR* 5.2 7.6 - - + +
130O ILE* 3.7 33.4 - - + +
131O PRO* 4.2 24.7 - - + -
160O GLN* 5.1 1.6 - - + +
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Residues in contact with VAL 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K LEU 2.9 16.8 + - - +
38K GLN* 3.3 9.9 - - - +
40K VAL* 1.3 76.5 - - - +
42K SER* 1.3 57.3 + - - +
44K LEU* 3.2 7.4 + - - +
45K LEU* 2.9 38.8 + - + +
58K VAL* 3.8 29.8 - - + +
61K LEU* 5.4 5.6 - - + -
62K THR* 3.3 29.4 - - + +
65K LEU* 4.7 14.1 - - + -
163O ILE* 5.0 15.9 - - + +
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Residues in contact with SER 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K GLN 2.9 13.4 + - - -
39K VAL* 3.2 10.7 + - - -
41K VAL* 1.3 78.0 - - - +
43K SER* 1.3 53.7 + - - +
45K LEU* 3.3 11.1 + - - +
46K THR* 2.7 41.7 + - - -
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Residues in contact with SER 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K VAL* 2.9 21.8 + - - +
40K VAL* 3.2 13.0 + - - -
42K SER* 1.3 77.0 - - - +
44K LEU* 1.3 60.1 + - - +
46K THR* 3.2 9.1 + - - -
47K GLU* 2.9 26.9 + - - +
118K VAL* 3.9 26.3 - - - +
119K ILE 5.1 3.5 + - - -
129O THR* 5.2 5.4 - - - +
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Residues in contact with LEU 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40K VAL* 3.0 31.1 + - + +
41K VAL* 3.2 4.0 + - - +
43K SER* 1.3 77.5 - - - +
45K LEU* 1.3 62.1 + - - +
47K GLU* 3.5 8.0 + - + +
48K ALA* 2.9 25.8 + - - +
65K LEU* 5.9 0.9 - - + -
110K TYR* 3.8 20.0 - - - +
114K SER* 6.4 0.9 - - - -
118K VAL* 4.8 15.7 - - + -
129O THR* 6.3 2.0 - - + -
160O GLN* 3.7 30.1 - - + +
163O ILE* 3.7 39.3 - - + -
164O SER* 4.1 8.9 + - - +
167O ALA* 4.8 3.6 - - - +
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Residues in contact with LEU 45 (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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41K VAL* 2.9 35.1 + - + +
42K SER* 3.7 10.3 - - - +
43K SER 3.3 0.2 - - - -
44K LEU* 1.3 76.7 - - + +
46K THR* 1.3 54.6 + - - +
48K ALA* 3.3 2.1 - - - +
49K GLY 2.5 32.2 + - - -
50K PHE* 3.2 46.4 + - + +
53K ALA* 4.8 11.2 - - + -
58K VAL* 4.5 18.8 - - + -
163O ILE* 6.0 4.5 - - + -
167O ALA* 4.6 11.0 - - + -
195O LEU* 5.5 11.2 - - + -
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Residues in contact with THR 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K SER* 2.7 26.4 + - - -
43K SER* 3.2 8.8 + - - -
45K LEU* 1.3 74.3 - - - +
47K GLU* 1.3 65.1 + - - +
49K GLY* 3.4 13.2 + - - +
50K PHE 5.3 2.2 - - - +
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Residues in contact with GLU 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K SER 2.9 16.4 + - - +
44K LEU* 3.7 12.8 - - + +
46K THR* 1.3 76.1 - - - +
48K ALA* 1.3 62.9 + - - +
110K TYR* 6.0 1.3 - - + +
113K ARG* 4.2 18.4 - - + +
117K MET* 3.1 64.4 - - - +
118K VAL* 3.3 18.4 - - + +
164O SER* 5.8 2.9 - - - +
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Residues in contact with ALA 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44K LEU 2.9 15.9 + - - +
45K LEU* 3.3 8.1 - - - +
47K GLU* 1.3 79.4 - - - +
49K GLY* 1.3 59.3 + - - +
50K PHE* 3.8 15.7 - - + -
167O ALA* 3.8 27.1 - - + +
168O ASN* 5.9 2.7 - - - +
171O LEU* 4.5 17.5 - - + +
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Residues in contact with GLY 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45K LEU 2.5 18.1 + - - -
46K THR* 3.4 10.5 + - - -
48K ALA* 1.3 75.8 - - - +
50K PHE* 1.3 63.3 + - - +
51K GLU* 3.4 3.6 + - - +
171O LEU* 5.7 2.2 - - - -
192O LYS* 5.7 0.5 - - - +
193O TYR* 3.9 17.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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