Contacts of the helix formed by residues 40 - 54 (chain A) in PDB entry 4Z2C
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ARG 3.6 18.7 + - - +
31A ALA* 3.2 18.8 + - - +
32A LEU 4.4 1.3 - - - -
33A PRO* 4.3 21.5 - - + -
39A LEU* 1.3 75.7 - - - +
41A PRO* 1.3 76.4 - - + +
42A VAL* 3.2 6.1 + - + +
43A HIS* 3.2 24.9 + - + +
44A ARG* 3.0 22.8 + - - +
169A ALA* 5.8 0.9 - - - +
170A THR 2.3 39.5 + - - +
171A GLY 3.5 3.0 - - - +
12E G 3.6 2.6 + - - -
13E T 2.8 36.1 + - - +
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Residues in contact with PRO 41 (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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28A VAL 5.1 1.3 - - - +
29A ALA* 3.6 34.5 - - + +
30A ARG* 4.1 14.4 - - - +
32A LEU 4.7 5.8 - - - +
39A LEU 4.6 0.7 - - - +
40A LYS* 1.3 88.0 - - + +
42A VAL* 1.3 57.0 + - + +
44A ARG* 3.5 19.3 + - - +
45A ARG* 2.9 61.4 + - - +
76A HIS* 4.6 4.7 - - + -
14E A 5.5 0.7 - - - +
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Residues in contact with VAL 42 (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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30A ARG 5.6 0.4 - - - +
40A LYS* 4.4 5.2 - - + -
41A PRO* 1.3 79.2 - - - +
43A HIS* 1.3 83.3 + - + +
45A ARG* 3.3 3.3 + - - +
46A ILE* 2.9 41.4 + - + +
76A HIS* 3.7 38.7 - - + +
82A SER 4.7 0.7 - - - +
83A ILE* 4.3 8.5 - - + -
86A ALA* 3.8 20.0 - - + -
13E T 3.9 25.4 - - - +
14E A 3.9 6.2 + - - +
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Residues in contact with HIS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.9 21.8 - - + -
40A LYS* 3.2 37.1 + - + +
42A VAL* 1.3 75.7 - - + +
44A ARG* 1.3 60.1 + - - +
46A ILE* 3.2 2.9 + - - +
47A LEU* 2.9 33.8 + - + +
86A ALA* 3.9 23.2 - - + +
89A ARG* 4.8 1.1 - - - -
90A MET* 3.7 27.3 - - + +
96A TYR* 3.6 22.1 + - - +
100A LEU* 5.9 0.4 - - + -
13E T 3.4 42.9 + - - -
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Residues in contact with ARG 44 (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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34A ASP* 3.7 13.9 - - - +
37A ASP* 3.1 27.3 + - - +
39A LEU* 2.8 40.0 + - + +
40A LYS 3.0 9.9 + - - +
41A PRO* 3.6 29.2 - - - +
43A HIS* 1.3 76.6 - - - +
45A ARG* 1.3 58.9 + - + +
47A LEU* 3.5 2.9 + - - +
48A TYR* 2.9 31.8 + - - +
154A PRO* 3.5 19.7 + - + +
155A LEU 3.2 29.0 + - - -
156A VAL* 3.9 6.3 - - - +
157A LEU* 3.8 20.9 - - + +
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Residues in contact with ARG 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 6.3 0.6 - - - +
41A PRO* 2.9 40.0 + - + +
42A VAL 3.7 4.0 - - - +
44A ARG* 1.3 77.7 - - + +
46A ILE* 1.3 59.9 + - - +
48A TYR* 4.6 4.3 - - + +
49A GLY* 2.9 26.0 + - - -
71A VAL* 3.6 15.9 - - + +
75A TYR* 3.3 44.1 + - + -
76A HIS* 3.0 30.7 + - + -
77A PRO* 3.4 12.5 - - - +
78A HIS* 4.7 2.6 - - - -
153A GLU* 2.9 38.8 + - + +
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Residues in contact with ILE 46 (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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42A VAL* 2.9 22.6 + - + +
43A HIS 3.2 4.7 + - - +
45A ARG* 1.3 78.1 - - - +
47A LEU* 1.3 58.7 + - - +
49A GLY 3.8 0.3 - - - -
50A MET* 2.9 41.3 + - + +
67A ILE* 5.0 1.3 - - + -
71A VAL* 3.9 10.1 - - + +
83A ILE* 3.3 46.7 - - + +
86A ALA* 3.8 12.8 - - + -
87A MET* 3.6 36.3 - - + +
90A MET* 3.7 20.2 - - + -
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.8 26.7 - - + -
43A HIS 2.9 14.5 + - - +
44A ARG 3.8 3.4 - - - +
46A ILE* 1.3 75.3 - - - +
48A TYR* 1.3 59.8 + - - +
50A MET* 3.2 7.6 + - - +
51A ASN 2.9 22.9 + - - -
90A MET* 3.8 18.8 - - + -
100A LEU* 3.9 27.6 - - + +
125A MET* 4.6 9.6 - - + -
129A ALA* 3.8 24.2 - - + -
132A MET* 4.4 14.8 - - + -
133A LEU* 3.5 17.0 - - + +
157A LEU* 4.2 14.4 - - + -
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Residues in contact with TYR 48 (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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44A ARG 2.9 17.9 + - - +
45A ARG* 4.4 3.8 - - + +
47A LEU* 1.3 75.8 - - - +
49A GLY* 1.3 57.0 + - - +
51A ASN* 3.1 13.3 + - - +
52A GLU* 2.9 60.9 + - + +
75A TYR* 3.4 43.0 + + - -
133A LEU* 4.3 9.3 - - + +
136A ILE* 4.8 10.3 - - + -
137A ASN* 6.1 0.4 - - - -
143A PHE* 3.5 20.3 - + - -
152A ARG 3.5 16.5 + - - -
153A GLU* 4.7 0.7 - - + -
154A PRO* 3.5 38.8 - - + -
157A LEU* 5.0 0.9 - - + -
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Residues in contact with GLY 49 (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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45A ARG 2.9 20.4 + - - -
46A ILE 3.9 0.4 - - - -
48A TYR* 1.3 77.6 - - - +
50A MET* 1.3 56.4 + - - +
52A GLU* 3.5 3.2 + - - +
53A LEU* 2.9 37.0 + - - +
67A ILE* 5.4 0.7 - - - -
70A ASP* 6.0 0.7 - - - -
71A VAL* 4.3 10.1 - - - -
74A LYS* 5.7 0.6 + - - -
75A TYR* 3.8 21.8 - - - -
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Residues in contact with MET 50 (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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46A ILE* 2.9 27.7 + - + +
47A LEU* 3.5 8.1 - - - +
48A TYR 3.2 0.2 - - - -
49A GLY* 1.3 73.8 - - - +
51A ASN* 1.3 64.5 + - - +
53A LEU* 3.3 1.3 + - - -
54A GLY 3.1 16.3 + - - -
55A VAL* 3.1 30.7 + - + +
67A ILE* 3.7 24.0 - - + +
87A MET* 3.6 38.8 - - + -
101A VAL* 4.2 15.3 - - + -
123A ALA* 3.9 16.8 - - + -
124A ARG 4.0 22.4 - - - +
125A MET* 4.0 15.9 - - + -
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Residues in contact with ASN 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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47A LEU 2.9 13.0 + - - +
48A TYR* 3.1 14.1 + - - +
50A MET* 1.3 77.1 - - - +
52A GLU* 1.3 69.8 + - - +
54A GLY* 3.0 18.7 + - - -
56A THR* 4.0 16.8 - - - +
125A MET* 4.1 8.7 - - - +
130A LEU* 5.3 3.3 - - - +
133A LEU* 3.8 24.9 - - + +
136A ILE* 3.6 28.9 - - - +
137A ASN* 5.3 2.6 + - - +
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Residues in contact with GLU 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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48A TYR* 2.9 60.0 + - + +
49A GLY 4.0 3.6 - - - +
51A ASN* 1.3 85.2 + - - +
53A LEU* 1.3 62.5 + - - +
54A GLY* 3.1 0.9 + - - -
74A LYS* 4.2 12.4 + - - +
75A TYR* 3.6 16.8 - - - +
137A ASN* 5.0 7.3 + - - +
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Residues in contact with LEU 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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49A GLY 2.9 23.2 + - - +
50A MET* 3.5 8.1 - - - +
51A ASN 3.1 0.4 - - - -
52A GLU* 1.3 78.2 - - - +
54A GLY* 1.3 60.9 - - - +
55A VAL* 3.7 17.5 - - + +
62A LYS* 5.5 7.4 - - + -
66A ARG* 3.9 34.5 - - + +
67A ILE* 4.8 17.5 - - + +
70A ASP* 3.2 42.0 - - + +
74A LYS* 5.6 1.6 - - - +
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Residues in contact with GLY 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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50A MET 3.1 0.6 + - - -
51A ASN 3.0 16.5 + - - -
52A GLU 3.1 1.5 - - - -
53A LEU* 1.3 79.1 - - - +
55A VAL* 1.3 58.7 + - - +
56A THR* 3.1 18.5 + - - -
59A LYS* 3.1 21.0 - - - +
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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