Contacts of the helix formed by residues 83 - 101 (chain A) in PDB entry 5HL0
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 TYR 83 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 4.4 19.0 + - + +
78A LYS 3.1 28.3 - - - -
79A ASN* 2.9 37.4 - - + +
80A SER 3.6 10.5 - - - +
81A PRO* 3.9 2.7 - - + +
82A PRO* 1.3 71.3 - - - +
84A ILE* 1.3 64.6 + - - +
85A LEU* 3.1 39.5 - - + +
86A ASP* 3.0 39.2 + - + +
87A LEU* 2.9 31.6 + - - +
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 3.9 24.5 - - + -
67A VAL* 4.9 0.6 - - - +
70A CYS* 3.8 21.3 - - + -
77A LEU* 3.7 27.6 - - + +
82A PRO 4.0 3.2 + - - -
83A TYR* 1.3 73.8 - - - +
85A LEU* 1.3 63.8 + - + +
87A LEU* 4.2 9.6 - - + -
88A LEU* 3.3 39.0 + - + +
129A THR* 5.0 0.4 - - + -
151A LEU* 4.4 11.0 - - + -
155A SER* 3.8 23.7 + - - +
158A PHE* 3.9 27.4 - - + -
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 3.8 37.1 - - + +
70A CYS* 3.8 27.8 - - + +
71A GLN* 4.0 20.0 - - + +
77A LEU* 4.6 4.0 - - + -
83A TYR* 3.1 39.0 - - + +
84A ILE* 1.3 83.4 - - + +
86A ASP* 1.3 61.6 + - - +
89A PRO* 3.1 23.1 - - - +
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Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASN* 4.1 5.2 - - - +
83A TYR* 3.0 34.1 + - + +
85A LEU* 1.3 80.5 - - - +
87A LEU* 1.3 66.7 + - + +
88A LEU 3.3 2.0 - - - -
89A PRO* 3.4 4.1 - - - +
90A ASP* 3.0 40.4 + - - +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PRO* 3.8 3.1 - - + -
83A TYR 2.9 36.8 + - - +
84A ILE* 3.5 8.5 + - - +
86A ASP* 1.3 78.4 - - + +
88A LEU* 1.3 58.0 + - + +
90A ASP* 3.4 6.4 + - - +
91A THR* 2.8 34.9 + - - +
155A SER 3.5 25.4 - - - +
158A PHE* 4.3 12.8 - - + -
159A SER* 3.7 31.9 - - - +
162A LEU* 4.0 19.0 - - + +
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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
----------------------------------------------------------
63A MET* 3.4 44.6 - - + +
66A VAL* 3.5 39.3 - - + -
67A VAL* 4.1 12.3 - - + -
84A ILE* 3.3 20.9 + - + +
87A LEU* 1.3 77.0 - - - +
89A PRO* 1.3 74.2 - - + +
91A THR* 3.2 3.1 + - - +
92A TYR* 3.0 21.3 + - - +
126A THR* 5.4 0.7 - - - +
158A PHE* 4.0 39.7 - - + -
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Residues in contact with PRO 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 4.3 13.2 - - + -
84A ILE 4.1 0.2 - - - +
85A LEU 3.1 30.1 - - - +
86A ASP* 3.4 6.7 - - - +
88A LEU* 1.3 94.5 - - + +
90A ASP* 1.3 59.9 + - - +
92A TYR* 3.3 11.9 + - + +
93A GLN* 3.0 33.9 + - + +
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Residues in contact with ASP 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASP* 3.0 37.5 + - - +
87A LEU* 3.7 5.8 + - - +
89A PRO* 1.3 77.5 - - - +
91A THR* 1.3 60.5 + - - +
93A GLN* 3.4 8.6 + - - +
94A HIS* 2.9 28.8 + - - +
162A LEU* 3.8 19.2 - - + +
166A LYS* 5.0 10.1 + - - +
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Residues in contact with THR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A MET* 3.4 26.7 - - + -
87A LEU* 2.8 20.2 + - - +
88A LEU* 3.2 3.1 + - - +
90A ASP* 1.3 73.0 - - - +
92A TYR* 1.3 61.3 + - - +
94A HIS* 3.2 2.8 + - - +
95A LEU* 2.8 43.8 + - + +
118A PHE* 4.6 13.0 - - + -
122A LEU* 4.3 13.0 - - + -
158A PHE* 4.9 6.2 + - - +
162A LEU* 3.5 27.5 + - + +
165A LEU* 4.7 1.6 - - + -
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Residues in contact with TYR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TRP* 3.3 68.8 - + + +
63A MET* 3.9 5.3 - - + +
88A LEU 3.0 13.2 + - - +
89A PRO* 3.4 15.3 - - + +
91A THR* 1.3 76.5 - - - +
93A GLN* 1.3 75.9 + - + +
95A LEU* 3.1 3.3 + - - +
96A ARG* 2.8 53.2 + - + +
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Residues in contact with GLN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO* 3.0 21.7 + - + +
90A ASP* 3.7 10.1 - - - +
92A TYR* 1.3 94.8 - - + +
94A HIS* 1.3 58.6 + - - +
96A ARG* 3.0 40.2 + - - +
97A THR* 2.9 30.4 + - - -
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Residues in contact with HIS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ASP 2.9 17.6 + - - +
91A THR 3.9 3.1 - - - +
93A GLN* 1.3 75.5 - - - +
95A LEU* 1.3 56.8 + - - +
97A THR* 3.2 14.6 + - + +
98A ILE* 3.0 35.6 + - + +
162A LEU* 4.5 5.8 - - + -
165A LEU* 3.8 30.9 + - + -
166A LYS* 3.9 35.7 - - + +
169A PHE* 2.9 29.0 + - - +
170A PRO* 5.0 0.7 - - + -
171A SER 4.5 9.0 - - - -
172A GLY 4.6 4.3 - - - -
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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
----------------------------------------------------------
56A VAL* 4.5 4.5 - - + -
60A TRP* 3.6 31.4 - - + +
63A MET* 4.7 0.7 - - - -
91A THR* 2.8 27.6 + - + +
92A TYR* 3.4 7.0 - - - +
94A HIS* 1.3 74.3 - - - +
96A ARG* 1.3 64.4 + - - +
98A ILE* 3.4 5.3 + - + +
99A LEU* 3.0 28.3 + - + +
115A PHE* 3.9 20.9 - - + -
118A PHE* 4.5 2.5 - - + -
119A MET* 3.8 28.0 - - + -
122A LEU* 3.8 27.6 - - + -
165A LEU* 4.3 15.5 - - + -
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Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TRP* 4.2 12.0 - - + -
92A TYR* 2.8 53.1 + - + +
93A GLN* 3.0 42.4 + - - +
95A LEU* 1.3 71.4 - - - +
97A THR* 1.3 63.9 + - - +
99A LEU* 3.4 6.7 + - - +
100A SER* 3.0 24.4 + - - -
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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
----------------------------------------------------------
93A GLN* 2.9 16.7 + - - -
94A HIS* 3.2 21.0 + - + +
96A ARG* 1.3 76.3 - - - +
98A ILE* 1.3 64.3 + - - +
100A SER* 2.8 25.1 + - - +
101A ARG* 3.1 10.9 + - + +
171A SER* 3.9 11.0 - - - +
172A GLY* 3.8 21.3 - - - +
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A HIS* 3.0 27.9 + - + +
95A LEU* 3.8 6.1 - - + +
97A THR* 1.3 74.1 - - - +
99A LEU* 1.3 65.9 + - - +
101A ARG* 3.1 6.9 + - - -
102A TYR* 3.1 25.6 - - + -
109A LEU* 3.8 32.3 - - + -
115A PHE* 4.3 15.3 - - + -
165A LEU* 3.7 24.2 - - + -
169A PHE* 3.6 32.3 - - + -
172A GLY* 3.5 29.4 - - - +
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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
----------------------------------------------------------
53A LYS* 5.2 11.0 - - + +
56A VAL* 4.3 26.7 - - + -
60A TRP* 3.9 29.8 - - + -
95A LEU* 3.0 18.8 + - + +
96A ARG* 3.6 5.6 - - - +
98A ILE* 1.3 78.1 - - + +
100A SER* 1.3 60.4 + - - +
102A TYR* 3.2 12.3 + - - +
103A GLU* 3.4 12.5 + - - +
106A MET* 3.8 32.6 - - + +
109A LEU* 3.8 15.0 - - + -
115A PHE* 5.2 4.7 - - + -
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Residues in contact with SER 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ARG 3.0 14.4 + - - -
97A THR* 2.8 22.9 + - - +
99A LEU* 1.3 76.8 - - - +
101A ARG* 1.3 66.9 + - - +
102A TYR 3.2 1.0 + - - -
103A GLU* 3.5 35.1 + - - +
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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
----------------------------------------------------------
97A THR* 3.1 12.5 + - + +
98A ILE 3.1 3.1 + - - +
100A SER* 1.3 82.1 - - - +
102A TYR* 1.3 62.3 + - - +
103A GLU 3.7 2.4 - - - +
105A LYS* 5.3 2.6 - - - +
171A SER* 2.8 51.7 + - - +
172A GLY 3.7 21.3 - - - +
173A LEU* 3.4 42.0 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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