Contacts of the helix formed by residues 90 - 102 (chain A) in PDB entry 1R4L
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 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLU* 4.2 7.9 - - - +
26A LYS* 4.2 1.3 - - - +
89A GLN* 1.3 78.4 - - - +
91A LEU* 1.3 67.6 + - - +
92A THR* 2.4 22.2 + - - -
93A VAL* 2.8 24.4 + - + +
800A NAG 1.5 77.5 + - - +
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Residues in contact with LEU 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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89A GLN 2.7 9.4 + - - -
90A ASN* 1.3 85.2 - - - +
92A THR* 1.3 92.2 + - - +
94A LYS* 3.1 23.9 + - + +
95A LEU* 3.2 13.9 + - + +
800A NAG 5.9 1.1 - - + -
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Residues in contact with THR 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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90A ASN* 2.4 14.8 + - - +
91A LEU* 1.3 85.1 - - - +
93A VAL* 1.3 57.9 - - + +
94A LYS 2.5 13.7 + - - -
95A LEU* 2.9 25.9 + - - +
96A GLN* 3.0 30.8 + - - +
389A PRO* 5.2 3.8 - - + -
392A LEU* 3.9 17.0 - - + -
563A SER* 5.0 10.4 + - - -
800A NAG 4.2 21.8 - - + +
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Residues in contact with VAL 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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22A GLU* 4.5 8.5 - - + -
25A ALA* 5.7 2.3 - - + +
26A LYS* 3.8 36.1 - - + +
29A LEU* 3.6 22.0 - - + +
88A ILE* 4.7 5.5 - - + +
89A GLN 3.0 18.8 - - - +
90A ASN* 2.8 44.1 + - + +
92A THR* 1.3 79.0 - - + +
94A LYS* 1.3 58.6 + - + +
96A GLN* 4.1 4.9 - - - +
97A LEU* 3.5 19.6 + - - +
800A NAG 3.9 12.6 - - - -
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Residues in contact with LYS 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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85A LEU 5.6 0.9 - - - -
86A GLN* 5.2 12.1 - - - +
88A ILE* 3.3 44.9 - - + +
89A GLN 4.3 4.3 - - - +
91A LEU* 3.1 17.4 + - - +
92A THR 2.5 5.5 + - - -
93A VAL* 1.3 74.1 - - - +
95A LEU* 1.3 62.7 + - - +
96A GLN 3.1 1.3 - - - -
97A LEU* 2.8 24.9 + - - +
98A GLN* 3.0 20.0 + - + +
211A GLY* 5.7 7.8 - - - -
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Residues in contact with LEU 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 LEU* 3.2 13.1 + - + +
92A THR* 2.9 22.7 + - - +
94A LYS* 1.3 76.6 - - - +
96A GLN* 1.3 79.0 + - - +
98A GLN* 2.9 43.3 - - - +
99A ALA* 3.6 4.7 + - - +
392A LEU* 3.4 38.3 - - + +
562A LYS 5.0 4.7 - - - +
563A SER* 5.0 15.7 - - - -
564A GLU 5.5 0.4 - - - +
565A PRO* 6.1 4.0 - - + -
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Residues in contact with GLN 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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29A LEU* 4.4 21.7 - - + +
33A ASN* 3.5 32.1 + - - +
92A THR* 3.0 31.6 + - - +
93A VAL* 4.1 8.6 - - - +
95A LEU* 1.3 83.8 - - + +
97A LEU* 1.3 63.5 - - - +
99A ALA* 3.7 14.4 + - - +
100A LEU* 4.1 9.5 + - - +
389A PRO* 3.5 27.4 - - - +
391A LEU* 4.0 17.2 - - + +
392A LEU* 3.8 19.0 - - + +
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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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25A ALA* 4.0 18.4 - - + -
28A PHE* 4.6 8.5 - - + -
29A LEU* 3.4 32.7 - - + +
80A ALA* 4.4 11.9 - - + +
83A TYR* 4.9 11.4 - - + +
84A PRO 5.6 0.9 - - - +
85A LEU 5.6 0.4 - - - +
88A ILE* 4.7 12.3 - - + -
93A VAL 3.5 10.1 + - - +
94A LYS* 2.8 16.1 + - - +
96A GLN* 1.3 79.8 - - - +
98A GLN* 1.3 64.9 + - - +
99A ALA 3.2 0.9 + - - -
100A LEU* 3.2 8.0 + - + +
101A GLN* 2.8 63.7 + - + +
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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
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94A LYS* 3.0 22.7 + - + +
95A LEU* 2.9 42.4 - - - +
97A LEU* 1.3 75.9 - - - +
99A ALA* 1.3 68.0 + - - +
101A GLN* 3.3 17.3 + - - +
102A GLN* 3.5 18.1 + - - +
210A ASN* 5.4 5.4 - - - +
211A GLY* 5.9 3.2 - - - +
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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 LEU 3.6 4.9 + - - +
96A GLN* 3.9 9.9 - - - +
97A LEU 3.2 0.6 + - - -
98A GLN* 1.3 82.9 - - - +
100A LEU* 1.3 64.2 + - - +
102A GLN* 3.0 26.4 + - - +
391A LEU* 4.2 26.0 - - + +
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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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28A PHE* 4.4 23.1 - - + -
29A LEU* 4.7 12.3 - - + -
32A PHE* 3.4 54.1 - - + -
73A LEU* 3.9 15.3 - - + +
76A GLN* 4.6 9.0 - - + +
77A SER* 3.2 22.7 + - - -
80A ALA* 4.2 11.2 - - + -
96A GLN 4.1 6.0 + - - +
97A LEU* 3.2 9.9 + - + +
99A ALA* 1.3 79.6 - - - +
101A GLN* 1.3 63.5 + - - +
102A GLN 3.1 4.7 + - - +
391A LEU* 4.0 13.7 - - + -
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Residues in contact with GLN 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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77A SER* 3.6 6.7 + - - -
80A ALA* 4.6 1.1 - - - -
81A GLN* 3.1 43.3 - - + +
83A TYR 4.0 16.5 + - - +
85A LEU* 4.5 20.2 + - - +
88A ILE* 5.8 0.2 - - - +
97A LEU* 2.8 44.9 + - + +
98A GLN* 3.7 12.7 - - - +
99A ALA 3.2 0.4 + - - -
100A LEU* 1.3 77.9 - - - +
102A GLN* 1.3 62.4 + - + +
103A ASN 3.2 1.7 + - - -
801A NAG 3.8 14.3 - - + +
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Residues in contact with GLN 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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77A SER* 3.7 1.8 + - - -
98A GLN* 3.6 15.8 - - - +
99A ALA* 3.0 16.4 + - - +
100A LEU 3.5 8.1 - - - +
101A GLN* 1.3 76.3 - - + +
103A ASN* 1.3 69.3 + - - +
104A GLY* 3.0 5.7 + - - -
194A ASN* 4.7 12.4 + - - +
195A HIS* 5.7 3.6 + - - +
196A TYR* 3.6 31.7 + - - -
202A TYR* 5.6 3.1 - - - -
801A NAG 5.3 1.8 - - - -
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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