Contacts of the helix formed by residues 98 - 108 (chain A) in PDB entry 1NN3
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 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.2 9.2 - - + +
10A VAL* 3.7 22.0 - - + -
12A GLU* 2.8 9.4 + - - +
42A PHE* 3.9 29.4 - + - -
76A ARG* 3.7 27.0 + - + +
83A ILE* 4.7 12.1 - - + +
95A VAL* 4.1 7.0 - - + -
97A ARG* 1.3 74.7 - - - +
99A ALA* 1.3 74.9 + - + +
100A PHE* 3.1 11.5 + + + -
101A SER* 3.2 10.9 + - - -
102A GLY 3.4 6.9 + - - -
124A LEU* 3.6 16.8 - - + +
125A PRO* 2.7 52.1 + - - +
127A PRO* 3.8 26.2 - - + -
210A LEU* 4.5 5.6 - - + -
301A 2DT 4.0 1.2 - - - +
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ARG* 3.7 9.4 - - - +
98A TYR* 1.3 83.7 - - + +
100A PHE* 1.3 58.9 + - + +
101A SER 3.3 0.2 - - - -
102A GLY* 3.1 2.1 + - - -
103A VAL* 2.9 31.9 + - - +
121A ASP* 3.3 32.6 - - + +
124A LEU* 4.1 4.7 - - + -
210A LEU* 3.7 26.7 - - + -
211A TRP* 4.1 6.7 - - + -
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Residues in contact with PHE 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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10A VAL* 4.2 5.2 - - + -
12A GLU* 3.3 30.1 - - + +
98A TYR* 3.1 13.1 + + + -
99A ALA* 1.3 75.1 - - - +
101A SER* 1.3 58.0 + - - +
103A VAL 3.3 0.9 + - - -
104A ALA* 2.9 30.7 + - - +
127A PRO* 4.1 15.7 - - + -
130A VAL* 3.9 29.2 - - + -
164A PHE* 3.8 9.9 - - + -
167A LEU* 3.7 16.4 - - + +
173A LEU* 3.6 31.9 - - + -
175A TRP* 3.8 22.7 - + + -
210A LEU* 4.0 14.1 - - + -
211A TRP* 3.7 24.0 - + - -
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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
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12A GLU* 2.6 30.7 + - - -
97A ARG* 2.8 41.9 + - - -
98A TYR 3.2 8.5 + - - -
100A PHE* 1.3 75.9 - - - +
102A GLY* 1.3 65.3 + - - +
105A PHE* 3.0 31.6 + - - +
164A PHE* 3.7 11.1 - - - -
301A 2DT 3.9 11.7 - - - -
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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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69A HIS* 3.4 19.4 + - - -
72A PHE* 5.4 0.7 - - - -
76A ARG* 3.9 10.3 - - - -
98A TYR 3.4 5.7 + - - -
99A ALA 3.1 8.0 + - - -
101A SER* 1.3 81.5 - - - +
103A VAL* 1.3 60.3 + - - +
106A THR* 3.4 17.3 + - - -
301A 2DT 3.0 27.8 + - - -
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Residues in contact with VAL 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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69A HIS* 5.0 0.2 - - + -
99A ALA 2.9 18.5 + - - +
100A PHE 3.9 2.9 - - - +
102A GLY* 1.3 74.3 - - - +
104A ALA* 1.3 63.1 + - - +
107A GLY* 2.8 29.5 + - - -
114A LEU* 3.7 30.4 - - + +
117A CYS* 3.6 36.1 - - + +
118A LYS* 3.7 10.5 - - + -
121A ASP* 4.8 3.6 - - - +
167A LEU* 3.9 17.9 - - + -
211A TRP* 3.6 21.3 - - + -
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A PHE 2.9 18.0 + - - +
101A SER 4.0 0.9 - - - +
103A VAL* 1.3 79.8 - - - +
105A PHE* 1.3 59.5 + - + +
108A ALA* 3.1 27.0 + - - +
160A ALA* 3.6 26.8 - - - +
163A CYS* 3.6 16.6 - - + -
164A PHE* 3.7 30.3 - - + +
167A LEU* 4.4 1.1 - - + +
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Residues in contact with PHE 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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97A ARG* 3.6 27.4 - - - -
101A SER* 3.0 22.7 + - - +
104A ALA* 1.3 75.3 - - + +
106A THR* 1.3 65.8 + - - +
108A ALA* 3.3 4.3 + - - -
109A LYS* 3.9 4.0 + - - +
151A TYR* 3.6 23.1 - + + -
156A PHE* 3.2 44.3 - + - -
157A GLN* 3.6 31.0 - - - -
160A ALA* 4.2 14.6 - - + -
164A PHE* 4.0 20.4 - + - -
301A 2DT 3.3 42.2 - + + +
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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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65A ASP 4.7 2.5 + - - +
68A VAL* 5.5 1.2 - - - +
69A HIS* 2.8 47.4 + - + +
72A PHE* 5.5 2.6 - - - -
102A GLY 3.4 9.2 + - - -
105A PHE* 1.3 77.6 - - - +
107A GLY* 1.3 56.2 + - - +
108A ALA 3.1 0.4 - - - -
109A LYS* 2.9 40.3 + - + +
112A PHE* 3.4 42.5 - - + +
117A CYS* 3.7 5.2 - - - -
151A TYR* 5.2 1.7 + - - -
301A 2DT 5.1 3.8 + - - -
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Residues in contact with GLY 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 VAL 2.8 20.1 + - - -
104A ALA 3.9 0.9 - - - -
106A THR* 1.3 77.4 - - - +
108A ALA* 1.3 58.9 + - - +
109A LYS 3.2 7.5 + - - +
112A PHE 4.0 14.3 - - - +
114A LEU* 4.7 5.7 - - - +
117A CYS* 3.9 12.7 - - - -
159A ARG* 5.0 3.6 + - - -
163A CYS* 3.5 18.9 - - - -
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Residues in contact with ALA 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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104A ALA 3.1 14.0 + - - +
105A PHE 3.4 12.8 - - - +
106A THR 3.1 0.4 - - - -
107A GLY* 1.3 77.6 - - - +
109A LYS* 1.3 59.7 + - - +
156A PHE* 3.6 23.3 - - + -
159A ARG* 2.7 52.9 + - + +
160A ALA 3.7 9.4 - - - +
163A CYS* 4.3 3.6 - - - -
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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