Contacts of the helix formed by residues 126 - 134 (chain O) in PDB entry 2AAZ
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 VAL 126 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82O TRP* 4.7 7.2 - - + -
87O CYS 5.3 0.2 - - - +
88O THR* 3.9 17.0 - - + +
101O TRP* 6.2 4.0 - - + -
123O LEU* 3.8 43.1 - - + +
124O GLY 2.8 15.7 + - - +
125O PRO* 1.3 74.3 - - - +
127O TYR* 1.3 83.8 + - + +
128O GLY 5.0 1.8 - - - +
129O PHE 2.8 16.6 + - - -
130O GLN* 3.3 6.4 + - - -
182O MET* 3.8 26.5 - - + -
183O ALA* 4.5 1.8 - - + +
184O LEU* 4.1 11.7 - - + +
186O PRO* 6.0 0.7 - - + -
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Residues in contact with TYR 127 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82O TRP* 5.3 0.4 - + - -
83O PHE* 3.4 34.8 - + + -
101O TRP* 3.7 29.9 - + - -
126O VAL* 1.3 83.5 - - + +
128O GLY* 1.3 67.0 + - - +
130O GLN* 3.0 3.3 + - - +
131O TRP* 2.9 33.2 + - - +
173O ALA* 3.9 22.6 - - + +
184O LEU 5.8 2.7 - - - -
185O PRO 4.3 1.7 + - - -
186O PRO* 3.5 27.0 - - + +
187O CYS* 2.7 23.0 + - - -
188O HIS* 3.2 40.1 - + + -
650O UMP 3.5 17.8 - - - -
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Residues in contact with GLY 128 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83O PHE* 3.1 33.6 - - - -
86O GLY* 3.2 21.6 - - - -
87O CYS 4.5 5.3 + - - -
126O VAL* 3.0 3.2 + - - +
127O TYR* 1.3 78.0 - - - +
129O PHE* 1.3 61.4 + - - +
131O TRP* 3.4 5.4 + - - +
132O ARG* 3.1 19.2 + - - +
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Residues in contact with PHE 129 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O GLY 3.6 11.7 + - - +
88O THR* 3.6 17.5 - - + +
125O PRO* 3.5 27.8 - - + -
126O VAL 2.8 15.8 + - - +
128O GLY* 1.3 72.3 - - - -
130O GLN* 1.3 64.5 + - - +
133O HIS* 2.6 60.8 + + + +
135O GLY 5.3 0.7 - - - -
136O ALA* 3.7 38.6 - - + -
138O TYR* 3.5 31.2 - + + -
145O TYR* 3.6 36.3 - + - -
178O ASP* 4.2 3.1 - - - -
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Residues in contact with GLN 130 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125O PRO* 3.0 31.4 + - - +
126O VAL 3.3 5.8 + - - +
127O TYR 3.0 4.8 + - - +
129O PHE* 1.3 82.6 - - - +
131O TRP* 1.3 62.4 + - - +
134O PHE* 3.1 35.5 + - + +
135O GLY 4.4 0.2 + - - -
152O GLN* 2.8 19.4 + - - -
172O SER 4.1 1.3 - - - +
173O ALA* 3.2 37.5 - - - +
175O ASN* 3.0 27.3 + - - +
178O ASP* 2.9 31.7 + - - +
182O MET* 4.3 1.5 - - + +
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Residues in contact with TRP 131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80O LEU* 4.6 8.1 - - + -
83O PHE* 3.6 44.6 - + + -
84O VAL* 4.4 12.3 - - + -
127O TYR* 2.9 21.0 + - + +
128O GLY* 3.5 8.7 - - - +
130O GLN* 1.3 78.6 - - - +
132O ARG* 1.3 64.8 + - - +
152O GLN* 3.0 31.2 + - - +
153O LEU* 3.4 15.2 + - + -
171O LEU* 3.8 38.4 + - + +
172O SER* 4.0 8.6 - - - +
173O ALA* 3.7 25.3 - - + +
188O HIS* 4.4 9.5 + + - -
190O PHE* 6.2 0.6 - - - +
230O SER* 6.1 0.2 - - - -
231O TYR* 3.4 27.5 + + - -
234O LEU* 4.0 24.0 - - + -
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Residues in contact with ARG 132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84O VAL* 2.7 46.7 + - - +
85O SER* 4.7 1.5 - - - +
86O GLY* 4.1 5.4 - - - +
128O GLY 3.1 15.8 + - - +
131O TRP* 1.3 80.3 - - + +
133O HIS* 1.3 86.4 + - + +
148O LYS 4.0 1.7 - - - +
149O GLY 4.6 0.2 - - - +
150O VAL 3.4 7.2 - - - +
151O ASP* 2.7 59.6 + - - +
153O LEU* 3.6 27.5 - - - +
154O GLN* 4.4 7.1 - - - +
292O ILE* 4.3 5.7 - - - +
293O ASP* 2.7 36.4 + - - -
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Residues in contact with HIS 133 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85O SER 5.2 3.0 + - - -
86O GLY* 4.8 11.2 + - - -
129O PHE* 2.6 45.4 + + + +
132O ARG* 1.3 96.9 + - + +
134O PHE* 1.3 66.4 + - - +
135O GLY 3.2 0.5 + - - -
136O ALA* 3.0 25.8 + - + +
145O TYR* 3.0 40.0 + + + +
146O LYS* 4.2 6.5 - - - -
147O GLY 4.6 2.5 - - - -
148O LYS 2.9 27.4 + - - +
149O GLY* 3.8 3.4 - - - -
150O VAL 3.8 1.1 - - - -
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Residues in contact with PHE 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130O GLN* 3.1 36.7 + - - +
133O HIS* 1.3 74.0 - - - +
135O GLY* 1.3 64.7 + - - +
149O GLY* 3.3 3.3 - - - -
150O VAL* 2.8 43.5 + - + +
152O GLN* 3.6 21.8 - - - +
172O SER* 4.3 5.8 - - - -
174O TRP 3.4 22.4 - - - -
175O ASN* 3.4 26.0 - - - -
134P PHE* 3.9 17.5 - + - -
174P TRP 5.0 0.2 - - - -
175P ASN* 3.7 15.0 - - - -
176P PRO* 3.5 36.8 - - + -
177P LYS* 4.1 6.9 - - + +
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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