Contacts of the helix formed by residues 89 - 101 (chain A) in PDB entry 4L2A
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 THR 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ALA* 3.8 9.9 - - + +
88A PRO* 1.3 81.6 - - - +
90A GLY* 1.3 70.5 + - - +
92A VAL* 4.2 1.2 - - - +
93A ALA* 3.3 12.1 + - - -
184A TRP* 4.0 15.8 - - + +
185A GLU* 4.8 9.8 + - - +
188A ASN* 2.9 24.1 + - - +
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Residues in contact with GLY 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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89A THR* 1.3 79.0 - - - +
91A ALA* 1.3 64.6 + - - -
93A ALA* 3.1 11.1 + - - +
94A ASP* 3.2 18.0 + - - +
188A ASN* 4.2 4.5 - - - -
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Residues in contact with ALA 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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90A GLY* 1.3 70.6 - - - -
92A VAL* 1.3 57.4 + - - +
94A ASP* 3.3 7.4 + - - +
95A ALA* 2.8 29.6 + - - +
188A ASN* 3.4 10.9 - - - +
191A PHE* 3.9 23.5 - - + -
192A ALA* 5.7 7.2 - - + -
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Residues in contact with VAL 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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89A THR 4.2 1.6 - - - +
91A ALA* 1.3 69.2 - - - +
93A ALA* 1.3 66.0 + - - +
95A ALA* 3.2 6.1 + - - +
96A ILE* 2.9 44.0 + - + +
125A LEU* 4.4 6.5 - - + -
133A LEU* 4.4 5.2 - - + -
153A ILE* 4.0 14.1 - - + -
184A TRP* 4.3 16.4 - - + -
187A ALA* 3.6 26.7 - - + +
188A ASN* 2.8 42.4 - - - +
191A PHE* 3.8 13.7 - - + -
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Residues in contact with ALA 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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88A PRO* 3.5 49.3 - - + +
89A THR* 3.3 6.6 + - - +
90A GLY 3.1 11.2 + - - +
92A VAL* 1.3 77.2 - - - +
94A ASP* 1.3 67.8 + - - +
96A ILE* 3.4 3.6 + - - +
97A ASN* 3.1 29.3 + - - +
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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
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90A GLY 3.2 13.9 + - - +
91A ALA* 3.8 8.5 - - - +
92A VAL 3.2 0.6 - - - -
93A ALA* 1.3 85.3 - - - +
95A ALA* 1.4 56.9 + - - +
97A ASN* 3.2 15.2 + - - +
98A ALA* 2.9 27.0 + - - +
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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 ALA 2.8 17.3 + - - +
92A VAL* 3.2 2.4 + - - +
94A ASP* 1.4 69.6 - - - +
96A ILE* 1.3 63.9 + - - +
98A ALA* 3.4 8.7 + - - +
99A LYS* 3.2 22.7 + - - +
133A LEU* 3.6 22.3 + - + +
191A PHE* 3.4 33.9 - - + -
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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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88A PRO* 4.1 15.7 - - + -
92A VAL* 2.9 33.9 + - + +
93A ALA* 3.6 5.2 - - - +
95A ALA* 1.3 74.4 - - - +
97A ASN* 1.3 69.2 + - - +
99A LYS 3.1 0.9 + - - -
100A TRP* 2.9 36.2 + - + +
102A SER 4.0 1.3 - - - +
103A PHE* 3.9 20.0 - - + +
106A PHE* 3.6 52.7 - - + -
125A LEU* 5.0 1.3 - - + -
133A LEU* 3.6 15.5 - - + -
184A TRP* 4.1 14.1 - - + -
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Residues in contact with ASN 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 ALA* 3.1 17.1 + - - +
94A ASP* 3.4 19.6 - - - +
96A ILE* 1.3 81.9 - - - +
98A ALA* 1.3 58.4 + - - +
101A GLY* 2.8 37.1 + - - +
102A SER* 3.4 23.4 - - - +
103A PHE* 3.5 13.1 - - - +
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Residues in contact with ALA 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 ASP 2.9 16.5 + - - +
95A ALA* 3.7 9.4 - - - +
96A ILE 3.1 0.8 - - - -
97A ASN* 1.3 78.7 - - - +
99A LYS* 1.3 60.3 + - - +
101A GLY 4.6 0.5 + - - -
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Residues in contact with LYS 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 3.2 10.8 + - - +
96A ILE 3.1 1.8 + - - -
98A ALA* 1.3 79.6 - - - +
100A TRP* 1.3 96.8 + - + +
101A GLY 3.6 0.4 + - - -
128A LEU* 6.5 0.2 - - - -
132A SER* 4.9 12.1 - - - -
133A LEU* 3.1 33.4 - - + +
134A ASP* 4.1 17.3 + - - -
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Residues in contact with TRP 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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96A ILE* 2.9 28.7 + - - +
99A LYS* 1.3 99.9 - - + +
101A GLY* 1.3 57.9 + - - +
102A SER* 3.1 20.7 + - - +
105A ALA* 3.6 17.0 - - + +
106A PHE* 3.3 52.5 - + + +
109A ALA* 3.8 20.6 - - + +
125A LEU* 3.9 3.8 - - + -
133A LEU* 3.7 34.1 - - + -
134A ASP* 3.9 28.7 + - - -
135A ILE* 3.5 23.2 - - + +
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Residues in contact with GLY 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 ASN* 2.8 28.1 + - - +
98A ALA 4.5 0.6 + - - -
99A LYS 3.6 1.6 - - - -
100A TRP* 1.3 74.7 - - - +
102A SER* 1.3 61.0 + - - +
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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