Contacts of the helix formed by residues 50 - 66 (chain A) in PDB entry 4KZZ
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 ASN 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A TYR 2.9 14.2 + - - +
38A ILE 4.5 0.2 - - - +
39A TYR* 2.4 68.9 - - - +
49A ILE* 1.3 74.4 - - - +
51A LEU* 1.3 65.2 + - - +
52A LYS* 3.1 10.0 + - + +
53A ARG* 3.3 38.8 + - + +
54A THR* 2.6 29.3 + - - -
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Residues in contact with LEU 51 (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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15A VAL* 4.5 24.5 - - + +
18A PHE* 4.2 22.7 - - + -
19A LEU* 4.4 16.8 - - + +
23A THR* 3.1 28.3 - - - +
24A HIS* 3.3 35.7 - - + +
49A ILE 3.0 8.4 + - - +
50A ASN* 1.3 73.2 - - - +
52A LYS* 1.3 52.6 + - - +
54A THR* 3.4 13.5 - - + +
55A TRP* 2.5 38.7 + - - +
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Residues in contact with LYS 52 (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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10A MET* 4.9 29.4 - - + -
50A ASN* 3.1 10.8 + - + +
51A LEU* 1.3 78.2 - - - +
53A ARG* 1.3 65.3 + - - +
55A TRP* 3.4 7.4 + - + +
56A GLU* 3.1 48.4 + - + +
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Residues in contact with ARG 53 (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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36A GLN* 2.5 66.5 + - - +
37A TYR* 3.4 34.0 + - + +
38A ILE 4.7 2.2 + - - -
50A ASN* 3.1 37.0 + - + +
52A LYS* 1.3 83.6 - - - +
54A THR* 1.4 63.5 + - - +
56A GLU* 3.4 7.9 + - - +
57A LYS* 3.2 31.7 + - + +
162A PRO* 4.8 1.3 - - - -
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Residues in contact with THR 54 (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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18A PHE* 4.9 6.5 - - + -
23A THR* 5.3 2.6 - - - +
49A ILE* 3.2 14.0 - - - +
50A ASN 2.6 13.3 + - - -
51A LEU* 3.4 21.2 - - + +
53A ARG* 1.4 70.6 - - - +
55A TRP* 1.3 67.0 + - - +
57A LYS* 4.2 0.3 - - - +
58A LEU* 3.3 18.5 + - - +
161A ILE* 3.8 4.2 - - + +
162A PRO* 2.7 48.7 + - - +
174A MET* 3.5 24.9 - - + -
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Residues in contact with TRP 55 (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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8A LEU 3.7 1.8 + - - -
9A GLN* 3.4 23.0 + - - -
10A MET* 4.1 22.9 - - + -
11A LYS* 5.5 1.1 - - + -
14A ASP* 2.5 29.6 - - + -
15A VAL* 6.2 4.0 - - + -
18A PHE* 3.0 49.6 - + + -
51A LEU 2.5 20.3 + - - +
52A LYS* 3.4 10.1 - - + +
54A THR* 1.3 75.6 - - - +
56A GLU* 1.3 73.7 + - + +
58A LEU* 2.9 22.5 + - + +
59A LEU* 3.1 47.9 + - + +
177A MET* 3.5 13.7 - - + -
180A ARG* 3.9 5.8 - - - -
181A GLU* 3.9 7.4 - - - -
184A ARG* 5.3 2.0 - - - -
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Residues in contact with GLU 56 (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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2A SER 5.1 8.3 + - - -
10A MET* 5.6 6.3 - - - +
52A LYS* 3.1 34.0 + - + +
53A ARG* 3.4 7.6 + - - +
55A TRP* 1.3 91.9 - - + +
57A LYS* 1.3 58.6 + - + +
59A LEU* 3.1 11.8 + - + +
60A LEU* 2.8 26.6 + - - +
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Residues in contact with LYS 57 (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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37A TYR* 3.8 30.2 + - + -
53A ARG* 3.2 20.5 + - + +
54A THR 4.2 2.2 - - - +
56A GLU* 1.3 75.7 - - + +
58A LEU* 1.3 55.7 + - - +
60A LEU* 2.9 10.6 + - + +
61A ALA* 2.6 35.3 + - - +
159A ILE* 3.4 29.3 - - + +
160A ALA 3.1 25.6 - - - +
161A ILE* 3.9 6.6 - - + +
162A PRO* 4.8 0.7 - - + -
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Residues in contact with LEU 58 (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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18A PHE* 4.5 9.6 - - + -
54A THR 3.3 12.7 + - - +
55A TRP* 2.9 18.3 + - + +
57A LYS* 1.3 77.9 - - - +
59A LEU* 1.3 57.5 + - + +
61A ALA* 3.3 1.2 - - - +
62A ALA* 2.9 23.3 + - + +
161A ILE* 3.6 13.6 - - + +
174A MET* 3.8 27.1 - - + +
177A MET* 3.5 32.8 - - + +
178A LEU* 2.0 52.5 - - + -
181A GLU* 5.0 4.7 - - + +
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Residues in contact with LEU 59 (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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8A LEU* 3.5 23.1 - - + +
55A TRP* 3.1 51.7 + - + +
56A GLU* 3.1 13.1 + - + +
58A LEU* 1.3 77.0 - - + +
60A LEU* 1.3 59.3 + - - +
62A ALA* 3.1 5.0 + - - +
63A ARG* 2.9 43.1 + - - +
181A GLU* 2.9 46.7 - - + +
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Residues in contact with LEU 60 (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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56A GLU 2.8 13.2 + - - +
57A LYS* 3.3 13.7 - - + +
59A LEU* 1.3 78.3 - - - +
61A ALA* 1.3 64.8 + - - +
63A ARG* 3.4 28.1 + - - +
64A ALA* 3.1 23.7 + - + +
145A ILE* 5.4 0.4 - - + -
159A ILE* 3.9 26.2 - - + -
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Residues in contact with ALA 61 (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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57A LYS 2.6 14.9 + - - +
58A LEU* 3.3 9.9 - - - +
60A LEU* 1.3 75.5 - - - +
62A ALA* 1.3 66.1 + - - +
64A ALA* 2.9 15.6 + - - +
65A ILE* 3.0 19.9 + - + +
145A ILE* 3.8 22.9 - - + +
159A ILE* 4.8 0.7 - - + -
161A ILE* 3.5 26.7 - - + -
178A LEU* 4.2 7.4 - - + -
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Residues in contact with ALA 62 (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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58A LEU* 2.9 13.8 + - + +
59A LEU 3.3 8.5 - - - +
61A ALA* 1.3 74.6 - - - +
63A ARG* 1.3 65.2 + - - +
65A ILE* 3.0 15.8 + - - +
66A VAL* 3.1 14.6 + - - +
178A LEU* 4.4 2.2 - - + +
181A GLU* 3.5 36.6 - - + +
182A VAL* 3.6 22.7 - - + +
185A MET* 5.4 2.2 - - + -
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Residues in contact with ARG 63 (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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4A ALA* 5.1 12.1 - - - +
8A LEU* 5.5 9.2 - - - +
59A LEU* 2.9 34.9 + - - +
60A LEU* 3.5 30.0 - - - +
62A ALA* 1.3 79.2 - - - +
64A ALA* 1.4 50.6 + - - +
66A VAL* 2.5 33.2 - - + +
67A ALA* 4.0 4.2 - - - +
185A MET* 3.6 43.3 - - + +
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Residues in contact with ALA 64 (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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60A LEU* 3.1 17.0 + - + +
61A ALA* 2.9 12.6 + - - +
63A ARG* 1.4 68.9 - - - +
65A ILE* 1.3 57.5 + - - +
66A VAL 2.7 17.5 - - - +
67A ALA* 4.3 3.9 - - - +
68A ILE* 3.5 18.4 + - - +
121A LEU* 3.9 10.9 - - + +
145A ILE* 4.7 13.0 - - + -
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Residues in contact with ILE 65 (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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61A ALA* 3.0 18.4 + - + +
62A ALA* 3.0 10.3 + - - +
64A ALA* 1.3 74.6 - - - +
66A VAL* 1.3 64.7 + - + +
68A ILE* 3.5 21.7 + - - +
71A PRO* 5.9 1.7 - - - +
74A VAL* 4.3 16.0 - - + +
90A PHE* 4.0 28.7 - - + -
94A THR* 5.6 4.3 - - - -
121A LEU* 3.6 21.8 - - + -
123A VAL* 4.3 16.8 - - + -
145A ILE* 5.1 1.6 - - + -
178A LEU* 5.0 11.0 - - + -
182A VAL* 3.8 26.2 - - + -
186A ARG* 5.1 0.3 + - - -
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Residues in contact with VAL 66 (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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62A ALA 3.1 10.0 + - - +
63A ARG* 2.5 28.2 - - + +
64A ALA 2.7 9.5 - - - +
65A ILE* 1.3 75.5 - - - +
67A ALA* 1.3 69.6 + - + +
68A ILE 3.2 0.2 - - - -
182A VAL* 3.7 13.2 - - + +
185A MET* 3.6 26.5 - - + -
186A ARG* 2.6 68.2 - - + +
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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
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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