Contacts of the helix formed by residues 83 - 103 (chain A) in PDB entry 4TZM
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 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A GLU* 4.3 17.5 + - - +
64A TYR* 3.3 36.7 - - + -
80A SER* 3.3 10.7 + - - +
81A PHE 4.6 0.2 - - - -
82A LYS* 1.3 76.4 - - - +
84A LEU* 1.3 58.2 + - - +
85A ARG* 3.1 16.1 + - - +
86A ALA* 3.2 18.8 + - + -
87A HIS* 2.8 30.5 + - - +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE 5.5 0.7 - - - +
82A LYS 3.5 7.0 + - - +
83A ASN* 1.3 73.8 + - - +
85A ARG* 1.3 59.6 + - - +
87A HIS* 3.3 15.9 + - + +
88A GLN* 3.0 27.3 + - - +
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Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.3 16.5 - - - +
64A TYR* 4.4 24.2 + - + -
83A ASN* 3.1 8.7 + - - +
84A LEU* 1.3 75.6 - - - +
86A ALA* 1.3 65.2 + - - +
88A GLN* 3.3 16.4 + - - +
89A ILE* 3.3 33.2 + - + +
494C THR* 5.1 7.7 + - - +
495C SER 3.0 27.1 + - - -
496C ILE* 3.7 24.4 - - - +
497C ASN 4.5 4.6 + - - +
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 3.3 34.2 - - + +
79A LEU* 3.9 14.9 - - + +
80A SER 3.3 15.5 - - - +
83A ASN* 3.2 18.2 + - + +
85A ARG* 1.3 77.1 - - - +
87A HIS* 1.3 59.2 + - - +
89A ILE* 3.3 13.8 + - - +
90A ALA* 3.0 26.7 + - - +
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Residues in contact with HIS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER 3.6 3.8 + - - -
81A PHE* 3.2 49.4 + + + +
83A ASN 2.8 18.0 + - - +
84A LEU* 3.4 18.8 - - + +
86A ALA* 1.3 78.0 - - - +
88A GLN* 1.3 60.2 + - - +
90A ALA* 3.3 4.8 + - - +
91A GLN* 3.1 47.7 + - + +
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Residues in contact with GLN 88 (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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84A LEU 3.0 11.9 + - - +
85A ARG* 3.6 20.1 - - + +
86A ALA 3.3 0.2 - - - -
87A HIS* 1.3 76.3 - - - +
89A ILE* 1.3 61.9 + - + +
91A GLN* 3.5 9.6 + - + +
92A LEU* 3.2 23.6 + - + +
493C ASN* 5.5 3.2 + - - -
494C THR* 4.2 32.5 + - + +
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Residues in contact with ILE 89 (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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54A LEU* 4.1 5.8 - - + -
60A LEU* 3.6 30.1 - - + -
64A TYR* 6.5 0.2 - - + -
79A LEU* 3.6 18.8 - - + -
85A ARG* 3.3 29.3 + - + +
86A ALA* 3.6 10.8 - - - +
87A HIS 3.3 0.2 - - - -
88A GLN* 1.3 76.4 - - + +
90A ALA* 1.3 65.1 + - - +
92A LEU* 3.1 19.4 + - + +
93A LEU* 3.0 21.3 + - + +
197A PHE* 3.9 27.6 - - + -
494C THR* 5.2 6.5 - - + -
496C ILE* 4.3 15.0 - - + -
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Residues in contact with ALA 90 (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 TYR* 4.0 17.3 - - + -
79A LEU* 4.2 6.0 - - + +
81A PHE* 3.7 31.9 - - + -
86A ALA 3.0 14.0 + - - +
87A HIS* 3.3 10.3 + - - +
89A ILE* 1.3 76.2 - - - +
91A GLN* 1.3 58.1 + - - +
93A LEU* 3.1 13.9 + - - +
94A ARG* 2.8 28.5 + - - +
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Residues in contact with GLN 91 (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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81A PHE* 5.8 1.6 - - + -
87A HIS* 3.1 45.0 + - + +
88A GLN* 3.7 9.1 - - - +
89A ILE 3.1 0.4 - - - -
90A ALA* 1.3 74.3 - - + +
92A LEU* 1.3 59.1 + - - +
94A ARG* 3.6 8.8 - - + +
95A ALA* 2.8 32.2 + - - +
212A ASP* 5.6 1.8 - - - +
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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
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88A GLN* 3.2 11.3 + - + +
89A ILE* 3.1 21.7 + - + +
91A GLN* 1.3 78.7 - - - +
93A LEU* 1.3 66.7 + - + +
95A ALA* 3.3 5.4 + - - +
96A ALA* 3.1 19.2 + - - +
197A PHE* 4.3 16.8 - - + -
212A ASP 4.6 0.7 - - - +
213A GLY* 3.9 35.9 - - - +
214A PHE* 3.6 23.8 - - + -
492C SER* 4.3 16.2 - - - -
493C ASN* 4.1 7.2 - - - +
494C THR* 3.7 26.7 - - + +
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE 5.1 2.1 - - - +
46A ILE* 4.1 28.6 - - + +
47A TYR* 4.2 26.0 - - + +
50A PHE* 4.1 20.6 - - + -
51A SER* 4.8 0.2 - - - +
54A LEU* 5.5 0.2 - - + -
79A LEU* 4.1 22.7 - - + -
89A ILE* 3.0 17.1 + - + +
90A ALA* 3.5 9.4 - - - +
92A LEU* 1.3 77.8 - - + +
94A ARG* 1.3 58.4 + - - +
96A ALA* 3.5 4.1 + - - +
97A GLY* 3.0 24.1 + - - -
108A ILE* 4.2 6.3 - - + -
197A PHE* 3.7 36.8 - - + -
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Residues in contact with ARG 94 (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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43A ILE* 3.6 27.8 - - - +
44A ARG* 6.3 0.4 - - - +
90A ALA 2.8 15.9 + - - +
91A GLN* 3.2 10.7 + - + +
93A LEU* 1.3 73.8 - - - +
95A ALA* 1.3 60.5 + - - +
97A GLY 3.3 0.9 + - - +
98A ASP* 2.8 56.9 + - - +
101A LYS* 5.1 7.5 - - - +
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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 GLN 2.8 15.4 + - - +
92A LEU 3.3 4.0 + - - +
94A ARG* 1.3 78.6 - - - +
96A ALA* 1.3 60.9 + - - +
98A ASP* 3.3 17.8 + - - +
99A ALA* 3.4 9.5 + - - +
211A ILE* 3.6 17.4 - - + +
212A ASP* 3.3 36.6 - - + +
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Residues in contact with ALA 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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46A ILE* 4.4 1.8 - - + -
92A LEU 3.1 13.5 + - - +
93A LEU 3.9 3.1 - - - +
95A ALA* 1.3 76.4 - - - +
97A GLY* 1.3 62.4 + - - +
99A ALA* 3.2 18.2 + - - +
100A THR 3.8 0.9 + - - -
105A LEU* 3.4 23.6 - - + +
108A ILE* 3.6 30.7 - - + -
199A LEU* 4.4 13.2 - - + -
211A ILE* 3.8 11.3 - - - +
214A PHE* 4.4 1.3 - - + -
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Residues in contact with GLY 97 (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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43A ILE* 3.2 26.5 - - - +
46A ILE* 3.7 21.0 - - - +
93A LEU 3.0 14.1 + - - -
94A ARG 3.6 3.6 - - - -
96A ALA* 1.3 75.4 - - - +
98A ASP* 1.3 60.4 + - - +
100A THR* 2.8 27.9 + - - -
101A LYS 4.1 0.2 + - - -
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Residues in contact with ASP 98 (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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43A ILE* 3.4 13.9 - - - +
94A ARG* 2.8 56.0 + - - +
95A ALA* 3.3 9.8 + - - +
97A GLY* 1.3 73.7 - - - +
99A ALA* 1.3 60.1 + - - +
100A THR 3.1 0.7 - - - -
101A LYS* 3.2 31.8 + - + +
102A ASP* 3.5 8.8 - - - +
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Residues in contact with ALA 99 (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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95A ALA 3.4 3.8 + - - +
96A ALA 3.2 13.4 + - - +
97A GLY 3.1 1.0 - - - -
98A ASP* 1.3 78.2 - - - +
100A THR* 1.3 58.4 + - - +
101A LYS 3.2 0.7 - - - -
102A ASP* 3.6 4.3 + - - +
103A GLY 3.1 5.7 + - - -
104A PHE* 2.9 28.4 + - - +
105A LEU* 3.6 12.3 + - + +
209A PHE* 4.2 18.6 - - + -
211A ILE* 3.6 32.8 - - + -
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Residues in contact with THR 100 (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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39A SER* 3.1 22.5 + - - -
42A MET* 4.3 8.5 - - + +
46A ILE* 4.7 0.4 - - + -
96A ALA 4.2 8.1 - - - +
97A GLY* 2.8 22.6 + - - +
99A ALA* 1.3 76.9 - - - +
101A LYS* 1.3 65.2 + - - +
102A ASP 3.4 0.2 - - - -
103A GLY* 3.3 6.4 + - - -
105A LEU* 4.2 12.6 - - + -
129A PHE* 4.2 22.4 - - + -
131A TYR* 3.4 35.9 - - - +
240A HIS* 3.5 16.8 + - - -
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Residues in contact with LYS 101 (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 ASP* 4.7 12.1 - - - +
39A SER* 3.0 22.9 - - - +
40A ASN* 3.0 32.1 + - - +
43A ILE* 3.7 21.5 - - + +
94A ARG* 5.1 6.5 - - - +
98A ASP* 3.2 22.2 + - + +
100A THR* 1.3 79.8 + - - +
102A ASP* 1.3 66.6 + - - +
103A GLY 3.4 0.5 + - - -
240A HIS* 5.3 0.4 + - - -
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Residues in contact with ASP 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASP 3.5 13.4 - - - +
99A ALA* 3.6 4.8 + - - +
100A THR 3.4 0.2 - - - -
101A LYS* 1.3 79.7 - - - +
103A GLY* 1.3 60.0 + - - +
104A PHE* 3.4 42.8 - - + -
140A ARG* 4.7 3.6 + - - -
209A PHE* 3.6 23.5 - - - -
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Residues in contact with GLY 103 (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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99A ALA 3.1 3.4 + - - -
100A THR 3.3 1.9 + - - -
101A LYS 3.1 3.8 - - - -
102A ASP* 1.3 81.1 - - - +
104A PHE* 1.3 63.1 + - - +
105A LEU 3.6 1.8 - - - -
131A TYR* 3.6 37.6 - - - -
140A ARG* 3.7 19.1 + - - -
202A THR* 3.3 11.4 + - - +
204A ASP* 4.1 4.0 - - - +
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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
------------------------------------------------------------
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