Contacts of the helix formed by residues 87 - 101 (chain A) in PDB entry 4RTN
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 CYS 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLU 3.9 9.6 - - - +
85A THR 3.1 4.1 + - - +
86A ASN* 1.3 77.7 - - - +
88A ALA* 1.3 67.8 + - - +
89A GLU* 4.1 14.6 - - - +
90A VAL* 3.4 34.4 + - - +
91A TYR* 3.0 21.7 + - - +
135A PHE* 3.6 12.2 - - - -
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Residues in contact with ALA 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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87A CYS* 1.3 73.1 - - - +
89A GLU* 1.3 76.4 + - - +
91A TYR* 3.1 1.9 + - - +
92A TYR* 3.0 47.3 + - + -
135A PHE* 3.8 27.0 - - + -
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Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A CYS* 4.1 13.4 - - - +
88A ALA* 1.3 90.4 + - - +
90A VAL* 1.3 62.9 + - + +
92A TYR* 3.7 5.6 + - - +
93A GLN* 3.4 20.6 + - - +
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU 3.8 9.0 - - - +
85A THR* 4.0 20.2 - - + +
87A CYS* 3.4 25.6 + - - +
88A ALA 3.3 0.4 - - - -
89A GLU* 1.3 75.7 - - + +
91A TYR* 1.3 67.0 + - - +
93A GLN* 3.3 6.2 + - + +
94A PHE* 3.0 50.8 + - + +
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Residues in contact with TYR 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 CYS 3.0 18.0 + - - +
88A ALA 3.1 3.6 + - - +
90A VAL* 1.3 78.2 - - - +
92A TYR* 1.3 72.4 + + - +
94A PHE* 3.3 3.8 + - - +
95A ARG* 2.8 31.6 + - - +
113A TYR* 3.5 27.5 + + - +
114A LEU* 3.6 19.9 + - + +
117A TYR* 3.8 6.5 - - + -
118A GLY* 3.3 29.8 - - - -
131A PHE* 3.8 13.7 - - - -
133A VAL* 2.7 30.2 + - - +
134A PRO 3.3 19.5 + - - -
135A PHE* 3.5 30.5 - + + -
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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
----------------------------------------------------------
88A ALA* 3.0 44.1 + - + +
89A GLU* 4.3 4.9 - - - +
91A TYR* 1.3 82.1 - + - +
93A GLN* 1.3 57.4 + - - +
95A ARG* 3.5 47.8 + - - +
96A GLU* 3.0 26.5 + - - +
134A PRO* 3.5 17.5 - - + +
135A PHE* 3.2 25.5 + - + +
11F G 3.6 22.9 + - - -
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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
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89A GLU 3.4 12.4 + - - +
90A VAL* 3.3 10.6 + - + +
91A TYR 3.2 0.2 - - - -
92A TYR* 1.3 76.6 - - - +
94A PHE* 1.3 62.8 + - + +
96A GLU* 3.2 8.5 + - + +
97A GLU* 2.8 32.2 + - + +
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Residues in contact with PHE 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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80A LEU* 4.3 18.2 - - + -
85A THR* 4.1 17.9 - - + -
90A VAL* 3.0 35.6 + - + +
91A TYR 3.6 7.4 - - - +
93A GLN* 1.3 79.5 - - + +
95A ARG* 1.3 55.4 - - - +
97A GLU* 3.3 25.3 + - - +
98A PHE* 2.9 29.5 + - - +
106A ARG* 3.7 14.1 - - - -
110A LEU* 3.6 18.8 - - + +
113A TYR* 3.5 36.3 - + + -
114A LEU* 4.5 2.0 - - + -
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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 TYR* 2.8 21.9 + - + +
92A TYR* 3.5 26.8 + - - +
93A GLN 3.2 0.2 - - - -
94A PHE* 1.3 76.5 - - - +
96A GLU* 1.3 60.4 - - - +
98A PHE* 3.6 2.6 + - - +
99A ASN* 3.1 31.1 + - - +
114A LEU* 3.8 15.6 - - + +
131A PHE* 3.3 38.4 + - + +
132A ASN* 3.2 18.7 - - - +
133A VAL 3.2 27.9 + - - +
10F C 4.8 1.6 - - - -
11F G 2.7 46.5 + - - -
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Residues in contact with GLU 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 TYR 3.0 17.4 + - - +
93A GLN* 3.6 9.3 - - + +
94A PHE 3.2 0.2 - - - -
95A ARG* 1.3 76.7 - - - +
97A GLU* 1.3 64.7 + - - +
98A PHE 3.2 0.2 - - - -
99A ASN* 3.2 8.0 + - + +
100A LYS* 3.1 60.0 + - + +
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Residues in contact with GLU 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 GLN* 2.8 19.8 + - + +
94A PHE* 3.4 22.0 - - - +
96A GLU* 1.3 76.4 - - - +
98A PHE* 1.3 57.0 + - - +
100A LYS* 3.4 4.9 + - - +
101A SER* 2.9 33.3 + - - -
106A ARG* 2.6 51.2 + - + +
110A LEU* 3.8 6.1 - - + -
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Residues in contact with PHE 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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58A ASP* 3.9 14.1 - - - -
94A PHE 2.9 17.6 + - - +
95A ARG 3.6 4.7 - - - +
96A GLU 3.2 0.2 - - - -
97A GLU* 1.3 77.4 - - - +
99A ASN* 1.3 75.4 + - - +
100A LYS 3.3 0.9 + - - -
101A SER* 3.4 9.0 + - - -
107A ARG* 2.8 92.0 + - + -
110A LEU* 3.5 17.7 - - + +
111A PHE* 3.8 28.9 - + + -
114A LEU* 3.9 15.0 - - + -
125A TYR* 5.0 2.7 - + - -
129A GLY 5.8 0.2 - - - -
131A PHE* 4.0 21.3 - + + -
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Residues in contact with ASN 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 ARG* 3.1 19.7 + - - +
96A GLU* 3.2 9.4 + - - +
98A PHE* 1.3 90.5 - - - +
100A LYS* 1.3 61.6 + - + +
101A SER 4.9 0.2 - - - +
107A ARG* 4.2 9.4 + - - +
129A GLY 4.1 2.4 - - - +
130A GLU* 3.4 31.8 - - + +
131A PHE* 2.9 47.1 + - - +
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Residues in contact with LYS 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 GLU* 3.1 51.7 + - + +
97A GLU* 3.8 5.2 - - - +
99A ASN* 1.3 81.4 - - + +
101A SER* 1.3 64.7 + - - +
102A GLN* 3.7 12.2 + - - +
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Residues in contact with SER 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU* 2.9 19.7 + - - -
98A PHE* 3.4 2.8 + - - -
99A ASN 4.9 0.2 - - - +
100A LYS* 1.3 79.6 - - - +
102A GLN* 1.3 66.2 + - - +
103A ASP* 3.2 21.9 + - - +
106A ARG* 3.8 20.4 - - - +
107A ARG* 3.2 39.0 + - - +
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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