Contacts of the helix formed by residues 93 - 107 (chain A) in PDB entry 4MCA
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 GLY 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ASP* 5.9 0.4 + - - -
40A VAL* 5.1 2.2 - - - +
92A GLY* 1.3 75.7 - - - -
94A GLY* 1.3 62.7 - - - -
95A LYS 3.4 2.2 - - - -
96A THR* 3.0 11.9 + - - -
97A LEU* 2.9 27.4 + - - +
116A THR* 4.1 1.0 + - - -
117A ILE* 4.2 19.5 - - - -
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Residues in contact with GLY 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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93A GLY* 1.3 71.6 - - - -
95A LYS* 1.3 57.6 + - - +
97A LEU* 3.3 10.2 + - - +
98A ASP* 2.8 39.4 + - - +
117A ILE* 4.7 6.5 - - - +
120A THR* 6.1 1.6 - - - -
122A ALA* 6.2 4.7 - - - -
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Residues in contact with LYS 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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64A PHE* 3.7 5.8 - - + -
66A GLY 3.4 27.8 - - - +
67A GLU* 3.7 30.5 + - - +
68A CYS* 4.0 15.0 - - + +
93A GLY 3.4 0.6 - - - -
94A GLY* 1.3 72.3 - - - +
96A THR* 1.3 65.9 + - - +
98A ASP* 4.6 2.0 - - - -
99A THR* 3.0 28.2 + - - -
131A TYR* 5.7 6.3 - - - -
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Residues in contact with THR 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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35A ILE* 3.4 31.7 - - + +
36A ALA* 4.2 2.0 - - - -
37A ASP* 4.4 10.2 + - - -
40A VAL* 5.7 0.2 - - - +
64A PHE* 3.2 27.1 - - + -
90A GLY 4.4 0.9 - - - -
91A VAL 3.3 33.4 + - - +
92A GLY* 4.7 0.2 - - - -
93A GLY 3.0 17.7 + - - -
95A LYS* 1.3 78.7 - - - +
97A LEU* 1.3 64.8 + - - +
99A THR* 3.2 2.9 + - - +
100A ALA* 3.0 20.8 + - - +
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Residues in contact with LEU 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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90A GLY 3.8 27.8 - - - +
92A GLY 3.9 17.0 - - - +
93A GLY 2.9 19.8 + - - +
94A GLY* 3.8 8.5 - - - +
96A THR* 1.3 77.5 - - - +
98A ASP* 1.3 60.4 + - - +
100A ALA* 3.1 4.2 + - - +
101A LYS* 3.0 34.0 + - - +
113A LEU* 3.8 20.5 - - + +
114A ILE 4.1 11.0 - - - +
115A PRO* 3.7 29.8 - - + -
122A ALA* 6.4 0.9 - - + -
123A PRO* 4.1 20.2 - - + -
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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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68A CYS* 3.8 21.8 - - + -
94A GLY* 2.8 25.4 + - - +
95A LYS* 4.1 2.1 - - - +
97A LEU* 1.3 71.4 - - - +
99A THR* 1.3 64.6 + - - +
101A LYS* 3.5 17.1 + - - +
102A ALA* 3.3 21.0 + - - +
122A ALA* 4.8 10.9 - - - +
127A LEU 3.7 10.0 - - - +
128A SER* 3.6 34.6 + - - +
129A VAL 4.3 7.4 + - - +
143A TYR* 4.4 0.2 + - - -
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Residues in contact with THR 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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35A ILE* 4.7 3.1 - - + -
64A PHE* 3.5 18.9 - - + -
68A CYS* 3.2 28.5 - - - +
72A GLU* 4.7 2.9 - - + -
73A ILE* 4.3 8.0 - - + +
76A LEU* 3.7 30.5 - - + -
95A LYS 3.0 17.8 + - - -
96A THR 3.4 4.5 - - - +
98A ASP* 1.3 79.2 - - - +
100A ALA* 1.3 63.0 + - - +
102A ALA* 3.2 5.2 + - - +
103A ILE* 3.0 30.6 + - + +
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Residues in contact with ALA 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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35A ILE* 4.0 14.4 - - + -
88A VAL* 3.7 17.3 - - + +
90A GLY* 3.7 31.2 - - - +
96A THR 3.0 9.9 + - - +
97A LEU 3.1 7.2 + - - +
99A THR* 1.3 75.4 - - - +
101A LYS* 1.3 64.4 + - - +
103A ILE* 3.3 1.4 + - - +
104A ALA* 2.9 26.0 + - - +
111A VAL* 3.9 3.3 - - + +
113A LEU* 4.0 7.0 - - + -
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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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97A LEU* 3.0 16.4 + - - +
98A ASP* 3.7 19.6 + - - +
99A THR 3.3 0.2 - - - -
100A ALA* 1.3 78.1 - - - +
102A ALA* 1.3 56.7 + - - +
104A ALA* 3.6 2.6 + - - +
105A HIS* 2.9 28.1 + - - +
111A VAL* 4.5 11.3 - - + +
113A LEU* 3.4 32.3 - - + -
122A ALA 3.0 23.6 + - - -
123A PRO* 3.6 4.7 + - - +
125A SER 2.8 29.3 + - - +
126A ALA* 5.4 0.2 - - - -
127A LEU 3.1 23.4 + - - +
143A TYR* 4.0 22.5 - - + -
147A PRO* 4.3 9.0 - - + -
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Residues in contact with ALA 102 (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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68A CYS* 5.7 0.7 - - - -
73A ILE* 3.6 34.5 - - + -
98A ASP 3.3 6.1 + - - +
99A THR 3.2 6.3 + - - +
101A LYS* 1.3 76.3 - - - +
103A ILE* 1.3 68.0 + - - +
105A HIS* 3.1 3.6 + - - +
106A TYR* 2.9 37.4 + - + -
143A TYR* 3.3 23.8 + - - +
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Residues in contact with ILE 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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33A LEU* 4.3 14.8 - - + -
35A ILE* 4.0 13.7 - - + -
73A ILE* 3.4 48.9 - - + +
76A LEU* 3.8 17.9 - - + -
77A GLY* 4.6 9.0 - - - +
80A LEU* 4.3 3.1 - - + -
88A VAL* 3.9 16.8 - - + -
99A THR* 3.0 24.7 + - + +
100A ALA 3.3 6.3 + - - +
102A ALA* 1.3 76.4 - - - +
104A ALA* 1.3 57.2 - - - +
106A TYR* 4.0 2.4 - - - +
107A GLN* 3.0 43.1 + - + +
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Residues in contact with ALA 104 (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 VAL* 3.8 15.7 - - + -
100A ALA 2.9 16.7 + - - +
101A LYS 4.0 2.5 - - - +
103A ILE* 1.3 73.5 - - - +
105A HIS* 1.3 61.7 + - - +
107A GLN* 4.9 0.2 - - - -
108A GLN* 2.9 8.8 + - - -
109A LEU* 2.9 49.9 + - - +
111A VAL* 3.5 26.0 - - + -
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Residues in contact with HIS 105 (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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101A LYS 2.9 19.6 + - - +
102A ALA 3.1 3.8 + - - +
104A ALA* 1.3 76.1 - - - +
106A TYR* 1.3 93.2 + + - +
108A GLN* 2.9 22.3 + - + +
143A TYR* 3.5 29.8 - + + +
144A PRO* 3.6 34.8 - - + +
145A ARG* 6.0 2.0 - - - +
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Residues in contact with TYR 106 (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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70A HIS* 3.8 27.3 + + - -
73A ILE* 3.9 26.5 - - + -
74A ASP* 5.7 1.3 - - - -
102A ALA* 2.9 38.2 + - + +
103A ILE* 4.1 3.1 - - - +
105A HIS* 1.3 96.5 - + - +
107A GLN* 1.3 72.9 + - - +
108A GLN* 3.4 7.6 + - - +
141A LEU* 5.4 8.4 - - + +
143A TYR* 5.4 2.7 - + - -
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Residues in contact with GLN 107 (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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77A GLY* 3.5 32.1 - - - -
80A LEU* 3.9 13.2 - - + -
81A LYS* 2.5 40.6 + - - +
103A ILE* 3.0 27.7 + - + +
104A ALA* 4.4 1.1 - - - +
106A TYR* 1.3 87.0 - - - +
108A GLN* 1.3 70.3 + - - +
109A LEU* 3.3 28.0 + - + +
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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