Contacts of the helix formed by residues 86 - 101 (chain A) in PDB entry 3NT7
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 LYS 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A TYR* 3.5 46.2 - - + +
71A PRO* 6.2 0.9 - - + -
72A LYS* 3.2 29.8 - - - +
73A ASP* 3.0 30.2 + - - +
80A GLU 5.3 0.2 - - - +
81A SER* 3.4 23.1 + - - +
84A PHE 3.8 0.2 - - - -
85A THR* 1.3 89.7 + - - +
87A LYS* 1.3 65.0 + - - +
88A SER 3.3 0.2 - - - -
89A ILE* 3.3 5.4 - - - +
90A LYS* 3.3 21.0 + - - +
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Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 5.2 0.2 - - - -
85A THR 3.5 5.8 + - - +
86A LYS* 1.3 71.8 - - - +
88A SER* 1.3 58.4 + - - +
90A LYS* 3.3 9.2 + - + +
91A GLU* 2.9 38.4 + - + +
183A ALA* 4.9 16.2 - - + -
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Residues in contact with SER 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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70A TYR* 3.8 23.9 - - - -
79A PHE* 4.7 10.0 - - - -
86A LYS 3.3 0.8 - - - -
87A LYS* 1.3 78.8 - - - +
89A ILE* 1.3 57.8 + - - +
91A GLU* 3.3 1.0 + - - +
92A ILE* 2.9 34.0 + - - +
181A HIS* 3.6 27.4 + - - -
182A PRO* 3.7 20.8 - - - +
183A ALA* 4.9 3.3 - - - +
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.5 3.8 + - - +
79A PHE* 3.4 38.1 - - + +
81A SER* 3.8 28.0 - - - +
84A PHE* 4.0 15.3 - - + -
86A LYS 3.3 11.9 + - - +
88A SER* 1.3 76.6 - - - +
90A LYS* 1.3 59.6 + - + +
92A ILE* 3.6 11.6 - - + +
93A ALA* 2.7 35.2 + - - +
108A TYR* 3.3 45.1 - - + +
109A ASN* 4.7 0.4 - - - -
110A LEU* 4.5 10.5 - - + +
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Residues in contact with LYS 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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84A PHE* 3.7 52.4 + - + +
85A THR* 3.7 25.6 + - - +
86A LYS 3.3 9.6 + - - +
87A LYS* 3.6 10.1 - - - +
89A ILE* 1.3 76.9 - - - +
91A GLU* 1.3 59.8 + - + +
93A ALA* 3.5 2.4 + - - +
94A SER* 2.9 31.9 + - - -
105A TYR* 4.8 0.5 + - - -
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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
----------------------------------------------------------
87A LYS* 2.9 21.7 + - + +
88A SER 3.7 3.4 - - - +
90A LYS* 1.3 75.5 - - + +
92A ILE* 1.3 60.7 + - - +
94A SER* 3.3 9.1 + - - -
95A SER* 2.9 32.2 + - - -
98A ARG* 4.4 9.0 + - - -
182A PRO* 3.3 26.9 - - - +
183A ALA* 4.4 8.5 - - + -
188A GLN* 4.9 6.1 + - - -
191A LYS* 3.5 18.5 + - - +
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Residues in contact with ILE 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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79A PHE* 4.0 25.8 - - + -
88A SER 2.9 22.9 + - - +
89A ILE* 3.6 9.2 - - + +
91A GLU* 1.3 76.4 - - - +
93A ALA* 1.3 56.5 + - - +
95A SER* 3.1 10.3 + - - -
96A ILE* 2.9 34.1 + - + +
108A TYR* 4.0 23.1 - - + -
110A LEU* 4.1 19.7 - - + -
158A LEU* 4.3 7.9 - - + -
182A PRO* 3.9 26.2 - - + -
195A PHE* 3.9 27.1 - - + -
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Residues in contact with ALA 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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84A PHE* 3.9 7.0 - - + -
89A ILE 2.7 20.9 + - - +
90A LYS 3.6 5.8 - - - +
92A ILE* 1.3 73.9 - - - +
94A SER* 1.3 56.3 + - - +
96A ILE* 3.3 3.0 + - - +
97A SER* 2.9 29.5 + - - -
105A TYR* 3.8 22.9 + - + -
108A TYR* 3.5 35.2 - - + -
216A PHE* 3.9 3.3 - - - -
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Residues in contact with SER 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 LYS 2.9 20.6 + - - -
91A GLU* 3.6 12.8 - - - -
92A ILE 3.2 0.2 - - - -
93A ALA* 1.3 71.5 - - - +
95A SER* 1.3 65.6 + - - +
97A SER* 3.4 4.4 + - - -
98A ARG* 3.0 49.7 + - - +
105A TYR* 3.8 12.9 + - - -
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Residues in contact with SER 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 2.9 16.3 + - - -
92A ILE* 3.2 12.0 - - - -
94A SER* 1.3 75.6 - - - +
96A ILE* 1.3 58.0 + - - -
98A ARG* 3.3 9.4 + - - +
99A LEU* 2.9 28.8 + - - +
191A LYS* 4.0 17.8 - - - +
192A ASP* 3.0 35.9 + - - +
195A PHE* 4.4 15.4 - - - -
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Residues in contact with ILE 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 ILE* 2.9 25.3 + - + +
93A ALA 3.3 4.2 + - - +
95A SER* 1.3 69.6 - - - +
97A SER* 1.3 54.0 + - - +
99A LEU* 3.2 6.5 + - + -
100A THR* 2.7 45.4 + - + +
108A TYR* 3.5 22.2 - - + +
195A PHE* 3.6 43.7 - - + -
212A TRP* 3.7 41.3 - - + +
216A PHE* 3.7 24.0 - - + -
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Residues in contact with SER 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA 2.9 17.5 + - - -
94A SER* 3.4 7.6 - - - -
96A ILE* 1.3 75.2 - - - +
98A ARG* 1.3 59.8 + - - +
100A THR* 4.0 1.1 - - - -
101A GLY* 2.8 31.9 + - - -
102A VAL 2.6 26.4 + - - +
103A ILE* 4.5 3.5 + - - -
105A TYR* 3.9 21.1 - - - -
216A PHE* 3.6 6.8 - - - -
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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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91A GLU* 4.4 6.5 + - - -
94A SER* 3.0 37.7 + - - +
95A SER* 3.3 19.2 + - - +
97A SER* 1.3 78.8 - - - +
99A LEU* 1.3 61.1 + - - +
101A GLY* 4.2 3.5 + - - -
188A GLN* 3.4 42.8 - - - +
191A LYS* 5.5 1.8 - - - +
192A ASP* 2.8 44.9 + - - +
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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
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95A SER 2.9 17.5 + - - +
96A ILE* 3.6 12.1 - - + +
98A ARG* 1.3 79.6 - - - +
100A THR* 1.3 65.1 + - + +
192A ASP* 3.7 26.2 - - + +
193A ARG* 4.7 11.0 - - - +
195A PHE* 3.7 22.2 - - + -
196A GLU* 3.7 39.9 - - + +
212A TRP* 4.6 9.6 - - + -
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Residues in contact with THR 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 ILE* 2.7 43.3 + - + +
99A LEU* 1.3 82.1 - - + +
101A GLY* 1.3 60.2 + - - +
102A VAL* 3.4 29.0 + - - +
211A ASN* 5.1 2.5 - - - +
212A TRP* 4.7 7.0 - - + +
213A ALA* 4.2 18.2 - - + +
216A PHE* 3.9 3.1 - - - -
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Residues in contact with GLY 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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97A SER 2.8 12.2 + - - -
98A ARG* 4.2 4.3 + - - -
99A LEU 3.6 2.2 - - - -
100A THR* 1.3 77.5 - - - +
102A VAL* 1.3 62.8 + - - +
103A ILE* 3.5 18.2 + - - +
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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