Contacts of the helix formed by residues 79 - 98 (chain A) in PDB entry 4TZJ
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 VAL 79 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LYS* 3.5 44.2 - - + +
61A CYS* 4.3 11.2 - - - -
76A GLN* 3.0 15.7 + - + +
77A SER 4.3 1.6 - - - -
78A SER* 1.3 80.4 - - - +
80A PRO* 1.3 64.2 - - + +
81A ALA* 3.8 17.7 - - + +
82A ALA* 2.9 30.2 + - + +
83A LYS* 2.9 12.3 + - - +
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Residues in contact with PRO 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A SER 4.8 0.2 - - - -
78A SER 3.4 9.4 - - - +
79A VAL* 1.3 87.4 - - + +
81A ALA* 1.3 57.6 + - - +
83A LYS* 3.5 11.8 - - + +
84A ARG* 2.9 58.5 + - - +
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 5.6 0.7 - - - -
60A LYS* 6.1 2.0 - - - -
61A CYS* 4.6 10.3 - - - -
79A VAL* 3.2 11.6 - - + +
80A PRO* 1.3 79.7 - - - +
82A ALA* 1.3 62.9 + - - +
84A ARG* 3.4 15.8 + - - +
85A VAL* 3.3 27.3 + - - +
661A ALA* 3.4 31.8 - - + +
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 5.3 1.8 - - - -
61A CYS* 3.5 35.1 - - + +
75A PHE* 4.2 8.2 - - + -
76A GLN 3.2 29.2 - - - +
79A VAL* 2.9 6.4 + - + +
81A ALA* 1.3 78.5 - - - +
83A LYS* 1.3 53.2 + - - +
85A VAL* 3.1 7.0 + - - +
86A SER* 2.7 38.0 + - - -
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Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLN 4.5 1.0 + - - -
77A SER* 3.6 41.4 + - - +
79A VAL 2.9 12.3 + - - +
80A PRO* 3.5 13.2 - - + +
82A ALA* 1.3 75.0 - - - +
84A ARG* 1.3 54.0 + - + +
86A SER* 3.6 7.7 - - - -
87A SER* 2.7 42.2 + - - +
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Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PRO* 2.9 37.7 + - - +
81A ALA* 3.4 19.0 - - - +
82A ALA 3.2 0.2 - - - -
83A LYS* 1.3 77.7 - - + +
85A VAL* 1.3 61.6 + - - +
87A SER* 3.5 15.3 + - - -
88A THR* 3.7 10.9 - - - +
660A VAL* 3.2 36.3 + - + +
661A ALA 3.0 24.6 + - - -
662A GLY* 4.1 13.7 + - - -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 4.1 14.4 - - + -
57A LEU* 4.1 11.7 - - + -
75A PHE* 3.7 28.0 - - + -
81A ALA 3.3 12.5 + - - +
82A ALA 3.1 6.8 + - - +
84A ARG* 1.3 73.4 - - - +
86A SER* 1.3 68.1 + - - +
87A SER 3.1 0.7 + - - -
88A THR* 2.9 28.9 + - + -
89A PHE* 3.8 2.8 - - - -
190A PHE* 4.5 10.8 - - + -
657A ILE* 3.7 33.9 - - + +
660A VAL* 4.3 9.2 - - + -
661A ALA* 4.4 4.9 - - + -
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Residues in contact with SER 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS* 3.1 33.0 + - - -
75A PHE* 3.8 29.5 - - - +
77A SER* 6.3 2.0 - - - -
82A ALA 2.7 21.1 + - - -
83A LYS* 3.6 10.1 - - - -
85A VAL* 1.3 73.4 - - - +
87A SER* 1.3 62.2 + - - +
88A THR 3.4 0.3 + - - -
89A PHE* 3.5 21.1 + - - +
90A ASP* 4.3 2.9 - - - +
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LYS* 2.7 25.7 + - - +
84A ARG* 3.7 9.3 - - - -
85A VAL 3.1 0.4 - - - -
86A SER* 1.3 74.0 - - - +
88A THR* 1.3 64.9 + - - +
89A PHE 3.0 3.1 - - - -
90A ASP* 3.0 36.6 + - - +
91A GLY 4.1 1.4 + - - -
205A GLU 5.3 0.9 - - - +
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Residues in contact with THR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG 3.7 11.4 - - - +
85A VAL* 2.9 24.7 + - + +
87A SER* 1.3 76.8 - - - +
89A PHE* 1.3 64.6 + - - +
90A ASP 3.5 0.3 + - - -
91A GLY 3.6 7.1 + - - -
92A LEU* 4.0 1.2 - - - +
190A PHE* 3.1 34.4 - - + -
205A GLU 4.1 5.5 - - - +
206A GLY* 5.5 6.7 - - - +
207A TYR* 3.3 30.4 + - - -
654A VAL* 4.7 13.7 - - + -
660A VAL* 4.6 10.8 - - + -
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Residues in contact with PHE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.8 12.7 - - + +
43A ILE* 4.1 7.6 - - + -
44A LYS* 3.9 39.0 - - + -
47A SER* 3.6 29.8 - - - -
75A PHE* 3.9 18.4 - + - -
85A VAL 3.8 3.8 - - - -
86A SER* 3.5 19.3 - - - +
87A SER 3.0 1.0 - - - -
88A THR* 1.3 91.5 + - - +
90A ASP* 1.3 60.2 + - - +
91A GLY 3.1 2.9 - - - -
92A LEU* 2.9 35.7 + - + +
93A ARG* 3.1 10.2 + - - +
104A PHE* 3.6 22.0 - + - -
190A PHE* 3.7 21.5 - + - -
207A TYR* 5.7 0.2 - - - -
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Residues in contact with ASP 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS* 4.6 7.3 + - - -
86A SER 4.3 4.7 - - - +
87A SER* 3.0 34.6 + - - +
89A PHE* 1.3 78.3 - - - +
91A GLY* 1.3 61.7 + - - +
93A ARG* 3.5 44.8 + - - +
94A ASP* 3.8 5.9 + - - +
205A GLU* 5.4 5.9 - - - +
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Residues in contact with GLY 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER 4.1 1.4 + - - -
88A THR 3.6 5.0 + - - -
89A PHE 3.1 0.6 - - - -
90A ASP* 1.3 78.6 - - - +
92A LEU* 1.3 62.3 + - - +
94A ASP* 3.4 9.8 + - - +
95A ALA 3.3 14.2 + - - -
202A TYR* 4.1 0.9 + - - -
204A PRO* 3.6 15.6 - - - +
205A GLU* 3.6 39.1 + - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.2 8.1 - - + -
43A ILE* 4.2 7.0 - - + -
88A THR 4.0 5.6 + - - +
89A PHE* 2.9 30.8 + - + +
91A GLY* 1.3 75.0 - - - +
93A ARG* 1.3 63.7 + - - +
95A ALA* 3.0 6.4 + - + +
96A ILE* 2.9 29.6 + - - +
101A LEU* 4.5 15.7 - - + -
104A PHE* 3.5 26.2 - - + -
192A VAL* 4.1 15.0 - - + -
204A PRO* 4.4 13.9 - - + -
207A TYR* 3.5 38.8 - - + +
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Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.3 40.3 - - + +
44A LYS* 5.3 6.7 - - - +
89A PHE 3.1 7.1 + - - +
90A ASP* 3.6 39.5 + - - +
91A GLY 3.3 0.6 - - - -
92A LEU* 1.3 75.8 - - - +
94A ASP* 1.3 63.0 + - - +
96A ILE* 3.3 13.4 + - - +
97A GLN* 3.3 26.2 + - + +
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ASP 3.8 5.6 + - - +
91A GLY* 3.4 11.6 + - - +
92A LEU 3.2 0.2 - - - -
93A ARG* 1.3 80.8 - - - +
95A ALA* 1.3 63.3 + - - +
96A ILE 3.2 1.4 + - - -
97A GLN* 3.5 15.3 + - - +
98A GLN* 3.0 41.7 + - - +
202A TYR* 4.0 9.7 + - - +
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Residues in contact with ALA 95 (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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91A GLY 3.3 8.0 + - - +
92A LEU* 3.0 18.0 + - + +
94A ASP* 1.3 79.8 - - - +
96A ILE* 1.3 56.7 + - - +
98A GLN 3.9 0.7 + - - -
99A GLY 3.7 1.0 + - - -
100A TYR* 2.9 31.4 + - + +
101A LEU* 3.2 20.6 + - + +
194A TYR* 5.8 0.7 - - + -
202A TYR* 3.4 32.9 + - + +
204A PRO* 4.4 7.2 - - + -
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Residues in contact with ILE 96 (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 GLU* 4.9 9.2 - - + +
39A ALA* 4.7 9.2 - - + -
40A LEU* 4.2 33.4 - - + +
43A ILE* 4.9 1.1 - - + -
92A LEU 2.9 19.5 + - - +
93A ARG* 3.3 5.6 + - - +
94A ASP 3.1 0.4 - - - -
95A ALA* 1.3 75.1 - - - +
97A GLN* 1.3 66.0 + - - +
98A GLN 3.1 1.6 - - - -
99A GLY 3.0 9.9 + - - -
101A LEU* 3.7 24.5 - - + -
125A PHE* 3.8 24.9 - - + -
127A TYR* 3.4 28.8 - - + +
233A HIS* 4.4 17.9 + - + +
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Residues in contact with GLN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU* 5.1 4.3 - - - +
36A GLU* 3.1 44.3 + - + +
93A ARG* 3.3 24.7 + - + +
94A ASP* 3.9 15.5 - - - +
96A ILE* 1.3 78.4 - - - +
98A GLN* 1.3 61.2 + - + +
99A GLY 3.3 3.1 + - - -
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Residues in contact with GLN 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASP* 3.0 36.9 + - - +
95A ALA 3.9 0.2 + - - -
96A ILE 3.1 0.6 - - - -
97A GLN* 1.3 81.3 - - + +
99A GLY* 1.3 61.5 + - - +
100A TYR* 3.1 49.3 + - + -
197A LYS* 3.0 23.9 + - - -
202A TYR* 5.1 4.2 - - - -
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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