Contacts of the helix formed by residues 60 - 78 (chain B) in PDB entry 4ZZ7
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 PRO 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ASN 3.5 7.2 - - - +
59B THR* 1.4 89.5 - - + +
61B PRO* 1.3 73.3 - - + +
62B LEU* 4.4 6.1 - - + +
63B LYS* 3.0 28.0 + - + +
64B ARG* 3.0 10.0 + - - +
125C ASN* 3.3 16.6 - - + +
126C VAL 4.5 5.6 - - - +
127C GLY* 3.8 5.6 - - - +
128C PRO* 3.8 39.3 - - + -
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Residues in contact with PRO 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B THR 3.8 4.3 - - - +
60B PRO* 1.3 83.6 - - + +
62B LEU* 1.3 56.8 + - - +
64B ARG* 3.7 26.0 - - + +
65B ALA* 2.9 31.2 + - - +
114B ALA* 4.5 3.0 - - + +
115B PRO* 4.2 24.4 - - + +
118B LEU* 4.2 22.7 - - + -
164B VAL 5.0 0.4 - - - +
124C ARG* 3.5 20.0 - - + +
125C ASN* 3.2 19.7 - - + +
446D TYR* 5.3 2.9 - - - +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PRO* 3.1 6.4 + - + +
61B PRO* 1.3 80.1 - - - +
63B LYS* 1.3 56.8 + - - +
65B ALA* 3.4 4.6 + - + +
66B ARG* 3.1 52.0 + - + +
115B PRO* 4.1 10.5 - - + +
125C ASN 5.9 0.2 - - - +
126C VAL 3.9 14.6 - - - +
106D GLU* 4.5 15.9 - - + +
109D GLU* 3.4 25.6 - - + +
444D VAL* 3.6 28.9 - - + -
446D TYR* 3.6 25.5 + - + +
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Residues in contact with LYS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TRP* 5.3 1.8 - - + -
59B THR* 3.8 21.1 - - + +
60B PRO* 3.0 21.4 + - + +
62B LEU* 1.3 76.3 - - - +
64B ARG* 1.3 67.1 + - - +
66B ARG* 3.3 25.3 + - + +
67B VAL* 3.7 10.6 + - - +
70B ARG* 5.3 2.4 + - - +
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Residues in contact with ARG 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TRP* 3.4 59.3 + - + +
57B ARG 3.2 21.4 + - - -
59B THR* 3.0 28.5 + - + +
60B PRO 3.0 16.3 + - - +
61B PRO* 3.7 19.2 - - - +
62B LEU 3.4 0.2 - - - -
63B LYS* 1.3 75.1 - - - +
65B ALA* 1.3 63.3 + - - +
67B VAL* 3.2 20.3 + - - +
68B MET* 3.8 4.0 + - - +
118B LEU* 3.6 18.2 - - - +
138B PRO* 4.7 1.4 - - - +
163B ILE* 3.8 2.0 - - - +
164B VAL* 2.8 39.1 + - + +
165B CYS 3.5 12.9 + - - -
166B GLY* 3.4 13.7 - - - +
124C ARG* 4.5 8.5 - - - +
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PRO 2.9 19.3 + - - +
62B LEU* 3.7 8.1 - - + +
63B LYS 3.2 0.2 - - - -
64B ARG* 1.3 78.0 - - - +
66B ARG* 1.3 58.5 + - - +
68B MET* 2.9 22.5 + - - +
69B PHE* 2.9 19.5 + - + -
111B ALA 4.3 0.2 - - - +
112B CYS* 3.4 29.2 - - - +
115B PRO* 4.5 7.0 - - + -
164B VAL* 3.7 15.7 - - + +
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 3.1 40.6 + - - +
63B LYS* 3.6 13.3 - - + +
64B ARG 3.2 0.6 - - - -
65B ALA* 1.3 77.1 - - - +
67B VAL* 1.3 60.7 + - - +
69B PHE* 3.2 16.6 + - + +
70B ARG* 3.2 49.1 + - - +
72D LYS* 5.3 4.7 - - - +
76D GLU* 5.9 1.6 - - - -
102D GLN* 4.2 19.1 - - - +
106D GLU* 3.4 27.1 + - - +
109D GLU* 2.6 51.4 + - - +
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TRP* 4.3 16.8 - - + -
63B LYS* 3.7 9.6 + - + +
64B ARG 3.4 13.0 - - - +
65B ALA 3.1 0.2 - - - -
66B ARG* 1.3 77.9 - - - +
68B MET* 1.3 62.6 + - - +
70B ARG* 3.0 24.4 + - - +
71B PHE* 2.8 24.9 + - - +
163B ILE* 6.2 0.4 - - + -
188B LEU* 4.5 10.8 - - + +
191B ALA* 3.7 17.7 - - + +
192B GLY 4.1 14.8 - - - +
193B LEU* 4.0 29.4 - - + +
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Residues in contact with MET 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG 4.3 2.5 - - - +
65B ALA 2.9 10.5 + - - +
67B VAL* 1.3 87.6 - - - +
69B PHE* 1.3 64.0 + - - +
71B PHE* 3.5 33.4 - - + -
72B LYS* 2.9 20.3 + - - +
108B VAL* 3.4 20.7 - - + +
111B ALA* 4.1 13.9 - - + -
112B CYS* 3.7 16.1 - - - +
159B PHE* 5.6 0.7 - - + -
160B PRO* 3.5 39.7 - - + +
163B ILE* 5.1 13.7 - - - -
164B VAL* 4.3 16.8 - - + -
188B LEU* 4.7 5.6 - - + -
193B LEU* 6.2 0.2 - - - -
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Residues in contact with PHE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA* 2.9 26.4 + - + -
66B ARG* 3.4 18.8 - - + +
67B VAL 3.2 0.2 - - - -
68B MET* 1.3 78.9 - - - +
70B ARG* 1.3 61.0 + - + +
72B LYS* 3.4 15.6 - - - +
73B GLU* 3.5 13.8 + - - +
112B CYS* 3.6 34.5 - - + -
69D PHE* 3.3 37.2 - + - -
72D LYS* 3.8 40.2 - - + +
109D GLU* 3.9 41.1 - - + -
112D CYS* 4.2 7.4 - - + -
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LYS* 5.3 2.8 + - - +
66B ARG* 3.2 38.5 + - - +
67B VAL* 3.0 28.5 + - - +
69B PHE* 1.3 76.0 - - + +
71B PHE* 1.3 66.0 + - - +
72B LYS 3.2 0.2 - - - -
73B GLU* 3.3 21.7 + - - +
74B LEU* 3.2 26.9 + - + +
190B GLU 5.2 2.2 - - - -
191B ALA* 2.6 48.9 + - + +
192B GLY* 4.0 6.5 + - - -
72D LYS* 6.2 2.0 - - - +
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Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL 2.8 15.5 + - - +
68B MET* 3.5 26.2 - - + +
70B ARG* 1.3 77.1 - - - +
72B LYS* 1.3 62.0 + - - +
74B LEU* 3.4 2.9 + - + +
75B LEU* 3.0 53.5 + - + +
108B VAL* 4.0 9.2 - - + -
156B LEU* 3.7 27.1 - - + -
159B PHE* 3.9 15.5 - + - -
184B ILE* 3.3 29.4 - - + -
187B LEU* 3.9 16.6 - - + -
188B LEU* 3.3 36.1 - - + -
191B ALA* 3.9 5.3 - - + +
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B MET 2.9 16.6 + - - +
69B PHE* 3.4 7.2 - - - +
70B ARG 3.2 0.2 - - - -
71B PHE* 1.3 78.4 - - - +
73B GLU* 1.3 63.0 + - + +
75B LEU* 3.6 7.0 + - - +
76B GLU* 2.3 62.7 + - - +
105B ILE* 3.7 15.2 - - + +
108B VAL* 4.0 12.5 - - + +
109B GLU* 3.2 37.8 + - + +
112B CYS* 5.2 0.7 - - - -
66D ARG* 5.3 6.6 - - - +
69D PHE* 3.6 42.3 - - + +
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PHE 3.5 10.4 + - - +
70B ARG* 3.3 27.3 + - - +
71B PHE 3.3 0.6 - - - -
72B LYS* 1.3 80.8 - - + +
74B LEU* 1.3 58.2 + - + +
76B GLU* 3.5 13.0 + - - +
77B GLN* 2.9 42.2 + - - +
72D LYS* 5.8 2.1 + - - -
73D GLU* 2.2 52.0 - - - +
76D GLU* 5.6 1.2 - - - +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ARG* 3.2 16.5 + - + +
71B PHE* 3.7 7.0 - - - +
72B LYS 3.3 0.2 - - - -
73B GLU* 1.3 74.9 - - + +
75B LEU* 1.3 59.9 + - - +
76B GLU 3.1 1.8 - - - -
77B GLN* 3.2 24.1 + - - +
78B HIS* 2.9 49.7 + - + +
187B LEU* 3.4 36.8 - - + +
190B GLU* 3.8 29.2 - - + +
191B ALA* 4.0 20.4 - - + +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PHE* 3.0 61.3 + - + +
72B LYS* 3.9 3.1 - - - +
73B GLU 3.5 0.2 - - - -
74B LEU* 1.3 77.2 - - - +
76B GLU* 1.3 61.2 + - - +
78B HIS 3.5 1.7 + - - -
79B ALA* 3.2 23.0 + - - +
82B ILE* 3.7 11.3 - - + +
101B LEU* 4.0 9.3 - - + +
105B ILE* 3.9 31.6 - - + -
108B VAL* 4.0 16.2 - - + -
156B LEU* 4.5 9.0 - - + -
184B ILE* 3.9 28.3 - - + -
187B LEU* 4.1 5.8 - - + -
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LYS* 2.3 46.2 + - - +
73B GLU* 3.5 13.9 - - - +
74B LEU 3.1 0.2 - - - -
75B LEU* 1.3 75.5 - - - +
77B GLN* 1.3 66.3 + - - +
79B ALA* 3.2 21.5 + - - +
102B GLN* 5.2 4.9 + - - +
105B ILE* 3.8 23.4 - - + +
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Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 2.9 33.1 + - - +
74B LEU* 3.2 24.5 + - - +
76B GLU* 1.3 76.4 - - - +
78B HIS* 1.3 69.3 + - + +
79B ALA 3.3 1.8 + - - -
80B ASP 5.2 0.2 + - - -
81B GLU* 4.0 7.1 - - - +
190B GLU* 5.5 0.3 - - - +
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Residues in contact with HIS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 2.9 42.0 + - - +
75B LEU 3.7 2.7 - - - -
76B GLU 3.2 0.2 - - - -
77B GLN* 1.3 88.3 + - + +
79B ALA* 1.3 63.5 + - - +
80B ASP 3.3 2.5 - - - -
81B GLU* 3.2 22.0 + - - +
82B ILE* 3.1 33.4 + - + +
183B TYR* 2.8 29.5 + - + +
187B LEU* 3.7 26.6 - - + +
190B GLU* 4.8 5.5 + - - -
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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
------------------------------------------------------------
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