Contacts of the helix formed by residues 94 - 110 (chain A) in PDB entry 3NYN
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 PRO 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A VAL 3.7 6.7 - - - +
93A THR* 1.3 94.4 - - + +
95A ASP* 1.3 67.7 + - - +
96A ASP* 3.4 15.9 - - - +
97A LYS* 3.2 10.2 + - + -
98A ARG* 3.0 19.2 + - - +
454A LYS* 6.0 0.2 - - - +
455A ARG* 3.7 14.1 - - - +
579A SO4 3.3 21.3 - - - +
555B LEU* 3.7 25.8 - - + +
556B PHE* 4.1 14.6 - - + -
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Residues in contact with ASP 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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94A PRO* 1.3 72.9 - - - +
96A ASP* 1.3 64.0 + - - +
98A ARG* 3.1 45.4 + - - +
99A LYS* 4.4 3.3 + - - +
137A PRO* 5.9 1.6 - - - +
139A LYS* 5.9 0.2 - - - -
579A SO4 3.4 20.4 + - - +
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Residues in contact with ASP 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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94A PRO* 4.2 10.9 - - - +
95A ASP* 1.3 79.4 - - - +
97A LYS* 1.3 88.0 + - + +
98A ARG 3.5 0.3 + - - -
99A LYS* 4.6 14.0 - - - +
100A ALA* 5.0 2.1 + - - +
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Residues in contact with LYS 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 THR* 3.9 18.8 - - + -
94A PRO* 3.2 12.2 + - + +
96A ASP* 1.3 94.0 + - - +
98A ARG* 1.3 63.7 + - - +
99A LYS 3.6 0.4 - - - -
100A ALA* 3.4 11.3 + - + +
101A CYS* 3.1 21.5 + - + +
554B ARG 4.1 13.0 + - - +
555B LEU* 4.5 8.3 - - - +
556B PHE* 5.2 0.7 - - - +
557B SER 3.2 45.5 + - - +
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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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90A TYR* 3.5 40.0 + - + +
91A GLU* 4.9 3.2 + - - +
93A THR* 3.5 25.0 + - - +
94A PRO 3.0 13.3 + - - +
95A ASP* 3.1 36.6 + - - +
96A ASP 3.3 2.0 - - - -
97A LYS* 1.3 76.5 - - - +
99A LYS* 1.3 52.6 + - - +
101A CYS* 3.0 4.8 + - - +
102A GLY* 2.6 33.8 + - - -
137A PRO* 3.0 34.2 + - + -
138A CYS* 4.1 11.7 - - - +
139A LYS* 4.1 27.5 - - - +
454A LYS* 4.6 3.8 - - - +
579A SO4 3.7 12.3 + - - -
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Residues in contact with LYS 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 ASP 4.4 3.0 + - - +
96A ASP 4.6 11.9 - - - +
98A ARG* 1.3 80.1 - - - +
100A ALA* 1.3 66.6 + - + +
102A GLY* 3.8 2.9 - - - +
103A ARG* 3.1 53.1 + - - +
133A LEU* 4.9 8.6 - - + +
134A GLU* 5.9 4.0 - - - +
137A PRO* 4.3 24.8 - - + +
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Residues in contact with ALA 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 ASP 5.2 1.6 - - - +
97A LYS* 3.4 14.3 + - - +
98A ARG 3.2 0.4 - - - -
99A LYS* 1.3 85.8 - - + +
101A CYS* 1.3 60.7 + - - +
103A ARG* 3.8 10.5 + - - +
104A GLN* 3.8 9.9 + - - +
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Residues in contact with CYS 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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86A GLY 5.2 0.9 - - - -
89A GLU* 5.0 11.0 - - - -
90A TYR* 4.3 19.7 - - - -
93A THR* 4.1 26.9 - - + -
97A LYS* 3.1 12.4 + - + +
98A ARG* 3.0 8.6 + - - +
100A ALA* 1.3 75.2 - - - +
102A GLY* 1.3 65.0 + - - +
104A GLN* 3.2 26.5 + - - +
105A LEU* 3.6 13.3 + - - +
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Residues in contact with GLY 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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90A TYR* 3.7 24.9 - - - -
98A ARG 2.6 20.2 + - - -
99A LYS* 3.3 3.5 + - - -
101A CYS* 1.3 73.8 - - - +
103A ARG* 1.3 58.9 + - - +
105A LEU* 3.4 8.7 + - - +
106A THR* 2.9 25.4 + - - -
133A LEU* 4.2 9.5 - - - +
142A PHE* 4.3 3.9 - - - -
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Residues in contact with ARG 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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99A LYS* 3.1 42.8 + - - +
100A ALA* 4.2 6.7 - - - +
101A CYS 3.3 0.4 - - - -
102A GLY* 1.3 73.0 - - - +
104A GLN* 1.3 56.9 + - - +
106A THR* 3.1 8.6 + - - -
107A GLN* 2.8 39.6 + - + +
133A LEU* 4.1 15.3 - - + +
134A GLU* 3.5 45.1 + - - +
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Residues in contact with GLN 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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100A ALA 3.8 7.3 + - - +
101A CYS* 3.2 18.1 + - - +
103A ARG* 1.3 77.2 - - - +
105A LEU* 1.3 61.9 + - + +
107A GLN* 3.6 5.8 + - - -
108A ASN* 2.7 54.2 + - - +
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Residues in contact with LEU 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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83A PHE* 5.2 4.9 - - + +
86A GLY* 3.6 41.3 - - - +
87A VAL* 3.9 13.0 - - + +
90A TYR* 4.1 17.7 - - + -
101A CYS* 3.6 15.2 + - - +
102A GLY 3.4 7.5 + - - +
103A ARG 3.1 0.4 - - - -
104A GLN* 1.3 80.0 - - + +
106A THR* 1.3 67.4 + - - +
108A ASN* 3.0 1.9 + - + -
109A PHE* 2.8 58.4 + - + +
110A LEU* 5.6 0.4 - - - -
142A PHE* 4.8 13.2 - - + -
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Residues in contact with THR 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 GLY 2.9 14.6 + - - -
103A ARG* 3.1 10.1 + - - -
105A LEU* 1.3 77.0 - - - +
107A GLN* 1.3 62.5 + - - +
110A LEU* 3.1 52.3 + - + +
129A CYS* 5.8 2.5 - - + -
130A THR* 4.6 24.9 - - + +
133A LEU* 3.5 19.6 - - + +
142A PHE* 4.4 10.4 - - - -
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Residues in contact with GLN 107 (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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103A ARG* 2.8 21.2 + - + +
104A GLN* 3.9 6.5 - - - +
106A THR* 1.3 74.7 - - - +
108A ASN* 1.3 69.6 + - - +
111A SER* 3.5 21.5 - - - +
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Residues in contact with ASN 108 (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 ARG* 4.4 6.1 + - - -
104A GLN* 2.7 48.7 + - - +
105A LEU* 3.7 2.5 - - - +
107A GLN* 1.3 86.7 + - - +
109A PHE* 1.3 81.2 + - + +
110A LEU 3.5 0.5 + - - -
111A SER* 4.1 7.3 + - - -
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Residues in contact with PHE 109 (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 ARG* 3.7 51.6 + - + +
82A ALA* 3.8 17.3 - - + -
83A PHE* 3.7 53.6 - + + -
105A LEU* 2.8 46.4 + - + +
108A ASN* 1.3 87.9 - - + +
110A LEU* 1.3 70.7 + - + +
111A SER 3.8 0.7 - - - -
117A LEU* 4.3 14.6 + - + +
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Residues in contact with LEU 110 (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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83A PHE* 5.5 2.9 - - + -
105A LEU 5.0 0.2 - - - +
106A THR* 3.1 41.2 + - + +
109A PHE* 1.3 93.1 - - + +
111A SER* 1.3 65.2 + - - +
112A HIS* 3.2 7.3 + - - +
117A LEU* 4.8 11.9 - - + -
121A VAL* 5.8 4.3 - - + -
126A VAL* 4.5 37.8 - - + +
129A CYS* 5.1 9.6 - - + -
130A THR* 6.1 0.4 - - - +
142A PHE* 5.0 9.0 - - + -
145A LEU* 4.1 32.8 - - + -
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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