Contacts of the helix formed by residues 89 - 103 (chain A) in PDB entry 4CAA
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 GLU 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A SER* 4.7 4.0 - - - +
66A LEU* 5.4 1.9 - - - -
68A ALA 5.0 0.3 - - - +
73A LEU* 3.3 32.4 - - + +
77A LEU* 4.7 14.1 - - + -
84A LEU* 4.9 5.6 - - + +
87A THR 3.9 1.0 + - - -
88A SER* 1.3 70.9 - - - +
90A ALA* 1.3 63.4 - - - +
92A ILE* 3.1 29.2 + - - +
93A HIS* 3.2 32.0 + - + +
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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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88A SER* 3.1 8.8 + - - +
89A GLU* 1.3 78.4 - - - +
91A GLU* 1.3 64.4 + - + +
93A HIS* 3.6 6.8 + - - +
94A GLN* 2.8 38.7 + - + +
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU 3.5 10.5 - - - +
87A THR* 3.1 28.8 + - + +
88A SER* 2.7 50.0 + - - +
90A ALA* 1.3 73.4 - - + +
92A ILE* 1.3 59.8 + - - +
94A GLN* 3.3 7.3 + - - +
95A SER* 3.1 21.9 + - - -
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Residues in contact with ILE 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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62A ALA* 5.2 2.7 - - + -
77A LEU* 3.7 38.1 - - + -
82A PHE* 3.7 50.9 - - + -
84A LEU* 4.7 2.5 - - + -
87A THR* 3.6 23.6 - - + +
88A SER 3.0 11.9 + - - +
89A GLU* 3.2 10.1 - - - +
91A GLU* 1.3 74.0 - - - +
93A HIS* 1.3 71.2 + - + +
95A SER* 3.1 23.8 + - - -
96A PHE* 3.4 16.3 + - + -
138A TYR* 5.0 0.2 - - - +
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Residues in contact with HIS 93 (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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62A ALA 3.6 16.2 - - - -
65A SER* 3.6 14.4 - - - -
66A LEU* 3.0 37.0 + - + +
77A LEU* 5.6 0.7 - - + -
89A GLU* 3.2 39.5 + - + +
90A ALA* 4.3 6.1 - - - +
92A ILE* 1.3 82.1 - - + +
94A GLN* 1.3 63.1 + - - +
96A PHE* 3.6 2.8 + - - +
97A GLN* 3.2 21.7 + - - +
137A LEU* 3.8 26.5 - - + +
138A TYR* 2.7 32.8 + - + +
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Residues in contact with GLN 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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90A ALA* 2.8 31.0 + - + +
91A GLU* 3.6 7.0 - - - +
92A ILE 3.3 0.2 - - - -
93A HIS* 1.3 75.8 - - - +
95A SER* 1.3 65.4 + - - +
97A GLN* 3.2 33.2 - - - +
98A HIS* 3.2 8.5 + - - +
136A ARG* 3.2 29.2 + - - +
137A LEU* 4.0 8.8 - - - +
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Residues in contact with SER 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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30A ASN* 5.8 1.7 + - - -
82A PHE* 6.0 1.7 - - - -
91A GLU 3.1 10.9 + - - -
92A ILE* 3.1 14.9 + - - -
94A GLN* 1.3 71.1 - - - +
96A PHE* 1.3 64.1 + - - +
97A GLN 2.9 3.6 - - - -
98A HIS* 2.7 35.6 + - - +
99A LEU* 2.9 16.4 + - - +
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Residues in contact with PHE 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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30A ASN* 4.2 12.1 - - - -
55A LEU* 4.5 8.3 - - + -
58A SER* 4.0 23.8 - - - -
59A THR* 3.4 37.7 - - + -
62A ALA* 3.6 11.9 - - + -
82A PHE* 3.6 34.8 - + - -
92A ILE* 3.4 17.0 + - + -
93A HIS 3.6 1.3 + - - +
95A SER* 1.3 83.3 + - - +
97A GLN* 1.3 56.5 + - - +
99A LEU* 3.6 17.2 - - + +
100A LEU* 2.8 38.0 + - + +
138A TYR* 3.5 36.6 - + + +
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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
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93A HIS 3.2 11.6 + - - +
94A GLN* 3.2 25.0 - - - +
95A SER 2.7 4.6 + - - -
96A PHE* 1.3 75.1 - - - +
98A HIS* 1.3 65.2 + - + +
100A LEU* 3.1 3.8 + - - +
101A ARG* 3.0 60.6 + - + +
136A ARG* 3.2 34.2 + - - +
137A LEU* 3.2 42.0 + - + +
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Residues in contact with HIS 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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94A GLN 3.2 7.2 + - - +
95A SER* 2.7 16.7 + - - +
97A GLN* 1.3 78.8 - - + +
99A LEU* 1.3 65.4 + - - +
101A ARG* 3.0 22.7 + - + +
102A THR* 3.0 42.5 + - + +
379B THR* 5.1 14.6 - - + +
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Residues in contact with LEU 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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30A ASN* 4.7 4.9 - - - +
55A LEU* 3.9 37.2 - - + -
59A THR* 4.9 2.9 - - - +
95A SER* 2.9 16.0 + - - +
96A PHE* 3.6 19.3 - - + +
98A HIS* 1.3 80.2 + - - +
100A LEU* 1.3 64.4 + - + +
101A ARG 3.1 0.2 + - - -
102A THR* 3.1 7.7 + - - +
103A LEU* 2.7 47.8 + - + +
114A MET* 4.8 5.2 - - - -
379B THR* 5.6 9.9 - - + +
381B ASN* 3.7 31.6 - - - +
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Residues in contact with LEU 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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59A THR* 4.2 5.8 - - + -
96A PHE 2.8 29.3 + - - +
97A GLN 3.5 3.6 - - - +
99A LEU* 1.3 77.0 - - + +
101A ARG* 1.3 63.0 - - - +
103A LEU* 4.2 2.0 - - - -
104A ASN* 2.8 39.2 + - - +
114A MET* 3.6 40.4 - - + +
115A GLY* 5.6 0.4 - - - -
116A ASN* 3.5 30.3 - - - +
137A LEU 3.7 6.1 - - - +
138A TYR* 3.6 33.9 - - + +
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Residues in contact with ARG 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 GLN* 3.0 50.2 + - + +
98A HIS* 3.0 25.5 - - + +
100A LEU* 1.3 79.2 - - - +
102A THR* 1.3 66.2 + - + +
104A ASN* 3.4 16.8 + - - +
105A GLN* 5.1 0.5 - - - +
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Residues in contact with THR 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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98A HIS* 3.1 35.9 + - + +
99A LEU* 3.1 13.7 + - - +
101A ARG* 1.3 78.6 - - + +
103A LEU* 1.3 64.7 + - - +
105A GLN* 2.8 42.1 + - - +
379B THR* 5.2 7.8 + - - +
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Residues in contact with LEU 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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55A LEU* 4.6 4.7 - - + -
99A LEU* 2.7 39.6 + - + +
100A LEU* 3.8 5.4 - - - +
102A THR* 1.3 73.5 + - - +
104A ASN* 1.3 53.0 + - - +
105A GLN* 2.7 19.9 + - - +
112A LEU* 3.4 53.4 - - + +
113A SER 4.1 1.8 - - - +
114A MET* 3.5 42.0 - - + +
188A ILE* 5.2 1.3 - - + -
383B PHE* 3.7 26.2 - - + -
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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
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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