Contacts of the helix formed by residues 89 - 106 (chain A) in PDB entry 1YRT
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 ALA 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A ARG* 1.3 85.8 - - - +
90A PRO* 1.3 78.8 - - + +
91A GLU* 3.4 6.3 - - + +
92A VAL* 3.6 15.8 + - + +
93A ILE* 3.4 17.3 + - - +
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Residues in contact with PRO 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 ARG 4.5 1.1 - - - +
89A ALA* 1.3 86.9 - - + +
91A GLU* 1.4 65.8 + - - +
93A ILE* 3.6 5.6 + - + +
94A ALA* 3.0 24.5 + - - +
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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
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89A ALA* 3.4 4.1 - - + +
90A PRO* 1.4 76.3 - - - +
92A VAL* 1.3 72.7 + - + +
94A ALA* 3.0 9.3 + - + +
95A ARG* 2.8 64.4 + - + +
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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
----------------------------------------------------------
85A LEU* 4.1 22.7 - - + -
88A ARG* 3.8 38.6 - - + +
89A ALA* 3.7 29.4 - - + +
91A GLU* 1.3 91.0 - - + +
93A ILE* 1.3 63.9 + - - +
94A ALA 2.9 1.2 + - - -
95A ARG* 3.1 4.6 + - - +
96A ALA* 3.0 22.9 + - - +
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Residues in contact with ILE 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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80A PRO* 4.4 10.2 - - + +
81A ASN* 3.3 44.6 - - - +
85A LEU* 4.2 19.3 - - + +
86A PHE 4.6 2.7 - - - +
88A ARG* 3.0 39.7 - - + +
89A ALA 3.4 8.7 + - - +
90A PRO* 4.2 4.7 - - + +
92A VAL* 1.3 75.6 - - - +
94A ALA* 1.3 57.2 + - - +
96A ALA* 3.8 8.4 - - - +
97A ASP* 2.9 41.2 + - - +
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Residues in contact with ALA 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 PRO 3.0 16.7 + - - +
91A GLU* 3.1 15.9 - - - +
92A VAL 2.9 0.8 - - - -
93A ILE* 1.3 74.8 - - - +
95A ARG* 1.3 64.0 + - + +
97A ASP* 3.1 22.5 - - - +
98A ASN* 3.1 18.7 + - - +
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Residues in contact with ARG 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 GLU* 2.8 44.6 + - + +
92A VAL* 3.8 5.4 - - - +
94A ALA* 1.3 72.9 - - + +
96A ALA* 1.3 58.6 + - - +
98A ASN* 2.9 20.1 + - - +
99A ASP* 2.8 35.7 + - - +
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Residues in contact with ALA 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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64A ALA* 5.1 0.6 - - - +
65A LYS* 5.3 6.1 - - + +
80A PRO* 3.5 25.1 - - + -
85A LEU* 3.6 22.7 - - + -
92A VAL 3.0 15.6 + - - +
93A ILE 3.8 2.2 - - - +
95A ARG* 1.3 78.3 - - - +
97A ASP* 1.3 55.3 - - - +
99A ASP* 3.3 15.1 + - - +
100A VAL* 2.9 33.8 + - + +
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Residues in contact with ASP 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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78A VAL 4.9 0.3 - - - +
80A PRO* 3.4 23.5 - - - +
93A ILE* 2.9 31.4 + - - +
94A ALA* 3.1 14.3 - - - +
96A ALA* 1.3 77.6 - - - +
98A ASN* 1.3 63.2 + - - +
100A VAL* 3.4 4.8 + - - +
101A ASN* 2.9 38.0 + - - +
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Residues in contact with ASN 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 ALA* 3.1 18.8 + - - +
95A ARG* 2.9 20.8 + - - +
97A ASP* 1.3 76.9 - - - +
99A ASP* 1.3 68.0 + - - +
101A ASN* 3.1 9.9 + - - +
102A SER* 2.8 27.1 + - - -
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Residues in contact with ASP 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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63A HIS* 3.6 36.3 + - + +
64A ALA* 3.8 20.4 - - - +
65A LYS* 3.8 10.7 + - - -
95A ARG* 2.8 20.4 + - - +
96A ALA* 3.3 18.2 + - - +
98A ASN* 1.3 77.1 - - - +
100A VAL* 1.3 64.4 + - - +
102A SER* 3.2 14.3 + - - -
103A SER* 3.2 17.2 + - - -
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Residues in contact with VAL 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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64A ALA* 3.7 22.9 - - + -
65A LYS 5.6 0.4 - - - +
77A PRO 3.9 9.4 - - - +
78A VAL* 3.6 49.4 - - + +
80A PRO* 3.9 8.5 - - + -
96A ALA 2.9 19.7 + - - +
97A ASP* 3.6 8.1 - - - +
98A ASN 3.1 0.2 - - - -
99A ASP* 1.3 78.9 - - - +
101A ASN* 1.3 66.5 + - - +
102A SER 3.2 0.2 + - - -
103A SER* 3.2 3.5 + - - -
104A LEU* 3.2 30.4 + - + +
177A ILE* 4.1 10.3 - - + +
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Residues in contact with ASN 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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78A VAL* 5.8 1.4 - - - +
97A ASP* 2.9 33.0 + - - +
98A ASN* 3.1 8.8 + - - +
100A VAL* 1.3 77.6 - - - +
102A SER* 1.3 62.8 + - - +
104A LEU* 3.4 18.1 + - - +
105A ALA* 3.1 23.6 + - - +
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Residues in contact with SER 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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61A GLY 6.1 0.4 - - - -
98A ASN 2.8 17.3 + - - -
99A ASP* 3.5 8.3 - - - -
100A VAL 3.1 0.2 - - - -
101A ASN* 1.3 77.6 - - - +
103A SER* 1.3 59.6 + - - +
105A ALA* 3.2 3.7 + - - -
106A HIS* 2.6 48.2 + - - -
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Residues in contact with SER 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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61A GLY 4.2 5.0 + - - -
62A VAL* 3.7 27.9 - - - +
63A HIS 4.1 3.1 + - - -
64A ALA 4.7 0.5 + - - -
99A ASP 3.2 11.3 + - - -
100A VAL 3.7 6.7 - - - -
102A SER* 1.3 77.8 - - - +
104A LEU* 1.3 59.2 + - - +
106A HIS* 3.2 9.2 + - - +
108A HIS* 2.9 51.3 + - - +
177A ILE* 4.6 13.9 - - - +
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Residues in contact with LEU 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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78A VAL* 4.6 7.9 - - + -
100A VAL* 3.2 31.8 + - + +
101A ASN* 3.8 17.5 - - - +
103A SER* 1.3 76.4 - - - +
105A ALA* 1.3 61.4 + - - +
107A GLY 4.2 3.3 + - - -
108A HIS* 3.4 30.6 - - + +
109A THR 3.6 24.2 - - - +
110A ALA* 3.8 17.9 - - + +
177A ILE* 4.7 8.7 - - + -
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Residues in contact with ALA 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 ASN 3.1 12.9 + - - +
102A SER* 3.2 5.4 + - - +
104A LEU* 1.3 77.5 - - - +
106A HIS* 1.3 80.5 + - + +
107A GLY 3.6 2.6 + - - -
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Residues in contact with HIS 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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102A SER* 2.6 39.1 + - - +
103A SER* 3.2 6.3 + - - +
105A ALA* 1.3 95.7 - - + +
107A GLY* 1.3 56.0 + - - +
108A HIS* 3.3 21.3 + - + -
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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