Contacts of the helix formed by residues 83 - 98 (chain A) in PDB entry 1YFL
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 SER 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A LYS 3.9 4.5 - - - -
79A LEU* 3.2 10.6 - - - +
80A SER* 2.4 54.8 + - - -
81A LYS 3.7 0.2 - - - -
82A THR* 1.3 62.9 + - - +
84A LYS* 1.3 63.4 + - - +
86A GLU* 3.2 32.9 - - - +
87A PHE* 3.2 18.9 + - - +
109A HIS* 5.6 0.5 + - - -
127A PHE* 3.7 8.1 - - - -
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Residues in contact with LYS 84 (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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82A THR 3.0 12.0 + - - +
83A SER* 1.3 73.7 - - - +
85A GLU* 1.3 67.9 + - + +
86A GLU* 3.5 0.6 + - - -
87A PHE* 3.1 4.7 - - - +
88A LEU* 3.1 47.2 + - + +
127A PHE* 3.8 36.1 - - + +
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Residues in contact with GLU 85 (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 LYS* 1.3 82.4 - - + +
86A GLU* 1.3 77.9 + - - +
87A PHE 3.0 1.6 - - - -
88A LEU* 3.2 31.9 + - - +
89A LYS* 3.0 23.0 + - - +
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Residues in contact with GLU 86 (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 TYR* 3.4 32.4 - - - +
78A LYS* 3.7 9.6 - - + +
79A LEU* 3.5 18.4 - - + +
83A SER* 3.2 30.0 - - - -
84A LYS 3.5 0.3 + - - -
85A GLU* 1.3 90.5 + - - +
87A PHE* 1.3 64.5 + - - +
89A LYS* 3.4 7.0 + - - +
90A LEU 3.2 14.0 + - - -
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Residues in contact with PHE 87 (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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79A LEU* 3.7 8.5 - - + +
83A SER 3.2 12.7 + - - +
84A LYS 3.1 11.0 - - - +
86A GLU* 1.3 74.7 - - - +
88A LEU* 1.3 71.3 + - + +
89A LYS 2.7 16.6 + - - -
90A LEU* 2.8 17.0 + - + +
91A ARG* 2.9 23.0 + - - +
106A LEU* 4.1 17.9 - - + -
109A HIS* 3.3 46.7 - + + -
110A GLY* 3.9 4.5 - - - -
123A PHE* 4.2 10.5 - + - -
125A THR 3.7 19.1 - - - -
126A PRO 3.9 8.7 - - - -
127A PHE* 3.1 38.6 - + + -
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Residues in contact with LEU 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 LYS* 3.1 33.7 + - + +
85A GLU* 3.2 39.7 + - - +
87A PHE* 1.3 88.1 - - + +
89A LYS* 1.3 60.7 + - - +
91A ARG* 3.3 38.7 - - - +
92A GLU* 3.1 20.1 + - - +
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Residues in contact with LYS 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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77A TYR* 4.2 10.3 - - + -
85A GLU 3.0 11.9 + - - +
86A GLU* 3.5 11.7 - - - +
87A PHE 2.7 5.3 + - - -
88A LEU* 1.3 69.4 - - - +
90A LEU* 1.3 57.4 + - - +
91A ARG 2.9 3.6 - - - -
92A GLU* 2.7 30.6 + - - +
93A ASP* 2.8 19.7 + - - +
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Residues in contact with LEU 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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73A VAL* 5.1 0.2 - - + -
77A TYR* 3.3 34.6 - - + +
79A LEU* 3.5 16.6 - - + -
86A GLU 3.2 4.5 + - - +
87A PHE* 2.8 14.1 + - + +
89A LYS* 1.3 75.5 - - - +
91A ARG* 1.3 61.3 + - - +
93A ASP* 3.7 0.8 - - - +
94A TYR* 3.1 17.7 + - - +
102A LEU* 3.3 40.2 - - + +
105A VAL* 3.5 36.1 - - + -
106A LEU* 3.8 18.3 - - + +
109A HIS* 4.9 1.6 - - + -
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Residues in contact with ARG 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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87A PHE* 2.9 21.7 + - - +
88A LEU* 3.3 36.2 - - - +
89A LYS 2.8 1.0 + - - -
90A LEU* 1.3 74.1 - - - +
92A GLU* 1.3 68.3 + - - +
94A TYR* 2.7 15.1 + - - +
95A ASN* 2.8 29.6 + - - +
106A LEU* 3.7 12.9 - - + +
123A PHE* 3.6 35.3 + - + +
124A THR* 3.6 13.4 + - - +
125A THR 2.8 28.4 + - - -
126A PRO* 4.0 8.1 - - - +
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Residues in contact with GLU 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 LEU 3.1 8.5 + - - +
89A LYS* 2.7 15.9 + - - +
91A ARG* 1.3 74.1 - - - +
93A ASP* 1.3 66.6 + - - +
95A ASN* 3.0 14.5 + - + +
96A LYS* 2.7 62.3 + - + +
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Residues in contact with ASP 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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77A TYR* 2.3 42.8 + - - +
89A LYS* 2.8 17.2 + - - +
90A LEU 3.7 5.8 - - - +
92A GLU* 1.3 78.4 - - - +
94A TYR* 1.3 62.7 + - - +
96A LYS* 3.1 9.8 + - - +
97A THR* 2.8 35.8 + - + +
102A LEU* 4.0 10.3 - - + -
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Residues in contact with TYR 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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54A PRO* 3.8 17.7 + - - +
90A LEU 3.1 7.4 + - - +
91A ARG 2.7 14.1 + - - +
93A ASP* 1.3 72.4 - - - +
95A ASN* 1.3 63.1 + - - +
96A LYS 2.8 0.3 + - - -
97A THR* 4.0 3.6 - - - -
98A ARG* 2.6 68.0 + - - +
99A ASP 3.5 21.5 - - - -
100A PRO* 4.3 2.4 - - + +
102A LEU* 4.0 7.8 - - + +
103A LEU* 3.6 46.4 - - + +
106A LEU* 3.5 22.0 - - + -
117A ILE* 5.0 3.4 - - + -
121A GLY 4.9 6.0 + - - -
123A PHE* 3.7 29.2 - - + -
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Residues in contact with ASN 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 ARG* 2.8 46.2 + - - +
92A GLU* 3.3 12.0 - - + +
94A TYR* 1.3 79.0 - - - +
96A LYS* 1.3 59.4 + - + +
98A ARG* 2.9 24.3 + - - +
122A ASN* 2.9 35.4 - - - +
123A PHE* 2.9 30.8 + - - +
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Residues in contact with LYS 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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92A GLU* 2.7 61.4 + - + +
93A ASP* 3.7 8.9 + - - +
94A TYR 2.8 0.8 + - - -
95A ASN* 1.3 80.7 - - + +
97A THR* 1.3 68.5 + - + +
98A ARG* 3.5 4.7 + - - +
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Residues in contact with THR 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 ASP* 2.8 30.3 + - + +
94A TYR 3.8 0.2 + - - -
96A LYS* 1.3 75.8 - - + +
98A ARG* 1.3 71.3 + - - +
99A ASP* 3.3 25.3 + - - +
102A LEU* 3.7 9.1 - - + +
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Residues in contact with ARG 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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54A PRO* 6.2 1.4 - - - +
94A TYR* 2.6 53.0 + - + +
95A ASN* 2.9 20.9 + - - +
96A LYS 4.1 3.8 - - - +
97A THR* 1.3 76.4 - - - +
99A ASP* 1.3 57.5 + - - +
100A PRO* 2.9 16.1 - - - +
120A LYS 2.6 28.9 + - - -
121A GLY* 3.0 22.5 + - - -
122A ASN* 3.1 17.0 + - - +
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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