Contacts of the helix formed by residues 126 - 134 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82L TRP* 4.7 7.4 - - + -
87L CYS 5.3 0.2 - - - +
88L THR* 3.9 17.6 - - + +
101L TRP* 6.2 4.9 - - + -
123L LEU* 3.8 43.1 - - + +
124L GLY 2.8 15.3 + - - +
125L PRO* 1.3 74.0 - - - +
127L TYR* 1.3 83.6 + - + +
128L GLY 5.0 1.1 - - - +
129L PHE 2.8 16.3 + - - -
130L GLN* 3.3 7.0 + - - -
182L MET* 3.9 26.2 - - + -
183L ALA* 4.6 1.8 - - + +
184L LEU 4.1 11.2 - - - +
186L PRO* 6.0 0.4 - - + -
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Residues in contact with TYR 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L TRP* 5.3 0.4 - + - -
83L PHE* 3.4 35.0 - + + -
101L TRP* 3.6 31.4 - + - -
126L VAL* 1.3 85.2 - - + +
128L GLY* 1.3 66.8 + - - +
130L GLN* 3.0 2.8 + - - +
131L TRP* 2.9 32.6 + - - +
173L ALA* 3.9 22.8 - - + +
184L LEU 5.8 2.5 - - - -
185L PRO 4.3 1.1 + - - -
186L PRO* 3.5 27.3 - - + +
187L CYS* 2.7 23.2 + - - -
188L HIS* 3.2 46.9 - + + -
500L UMP 3.5 13.0 - - - -
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Residues in contact with GLY 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83L PHE* 3.1 34.0 - - - -
86L GLY* 3.2 23.0 - - - -
87L CYS 4.5 5.5 + - - -
126L VAL* 3.0 3.4 + - - +
127L TYR* 1.3 78.1 - - - +
129L PHE* 1.3 61.8 + - - +
131L TRP* 3.4 4.9 + - - +
132L ARG* 3.2 18.9 + - - +
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Residues in contact with PHE 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86L GLY 3.6 11.3 + - - -
88L THR* 3.5 18.8 - - + +
125L PRO* 3.5 28.0 - - + -
126L VAL 2.8 16.0 + - - +
128L GLY* 1.3 71.9 - - - +
130L GLN* 1.3 64.4 + - - +
133L HIS* 2.7 60.7 + + + -
135L GLY 5.3 0.7 - - - -
136L ALA* 3.7 36.1 - - + -
138L TYR* 3.6 29.8 - + + -
145L TYR* 3.6 36.1 - + - -
178L ASP* 4.2 3.6 - - - -
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Residues in contact with GLN 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125L PRO* 2.9 31.8 + - - +
126L VAL 3.3 5.4 + - - +
127L TYR 3.0 4.5 + - - +
129L PHE* 1.3 82.4 - - - +
131L TRP* 1.3 58.2 + - - +
134L PHE* 3.2 34.8 + - + +
135L GLY 4.5 0.2 + - - -
150L VAL 4.1 0.3 - - - +
152L GLN* 2.8 23.8 + - - -
172L SER 4.0 1.6 - - - +
173L ALA* 3.2 37.9 - - - +
175L ASN* 3.0 27.2 + - - +
178L ASP* 3.0 31.3 + - - +
182L MET* 4.3 1.7 - - + +
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Residues in contact with TRP 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80L LEU* 4.5 8.3 - - + -
83L PHE* 3.5 45.3 - + + -
84L VAL* 4.3 11.2 - - + -
127L TYR* 2.9 22.4 + - + +
128L GLY* 3.5 10.1 - - - +
130L GLN* 1.3 77.3 - - - +
132L ARG* 1.3 64.7 + - + +
152L GLN* 3.0 31.2 + - - +
153L LEU* 3.4 16.1 + - + -
171L LEU* 3.8 39.6 + - + +
172L SER* 4.0 8.6 - - - +
173L ALA* 3.7 24.6 - - + +
188L HIS* 4.4 10.2 + + - -
189L MET 6.3 0.2 - - - -
190L PHE* 6.3 0.4 - - - +
230L SER* 6.0 0.2 - - - -
231L TYR* 3.4 27.0 + + - -
234L LEU* 4.0 23.6 - - + -
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Residues in contact with ARG 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84L VAL* 2.6 47.3 + - - +
85L SER* 4.6 1.9 - - - +
86L GLY* 4.0 6.1 - - - -
128L GLY 3.2 16.2 + - - +
131L TRP* 1.3 80.1 - - + +
133L HIS* 1.3 85.6 + - + +
148L LYS 3.9 1.7 - - - +
149L GLY 4.7 0.2 - - - +
150L VAL 3.4 7.6 - - - +
151L ASP* 2.7 58.4 + - - +
153L LEU* 3.6 28.0 - - - +
154L GLN* 4.4 7.7 - - - +
292L ILE* 4.3 6.2 - - - +
293L ASP* 2.8 36.6 + - - -
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Residues in contact with HIS 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85L SER 5.2 3.0 + - - -
86L GLY* 4.7 11.3 + - - -
129L PHE* 2.7 46.5 + + + +
132L ARG* 1.3 96.4 + - + +
134L PHE* 1.3 66.5 + - - +
135L GLY 3.2 0.3 + - - -
136L ALA* 3.0 26.0 + - + +
145L TYR* 3.0 41.8 + + + +
146L LYS* 4.2 6.5 - - - -
147L GLY 4.6 2.9 - - - -
148L LYS 2.9 27.2 + - - +
149L GLY* 3.8 2.5 - - - -
150L VAL 3.8 1.8 - - - -
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Residues in contact with PHE 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134K PHE* 3.9 17.9 - + - -
174K TRP 5.0 0.2 - - - -
175K ASN* 3.6 15.7 - - - -
176K PRO* 3.5 41.5 - - + -
177K LYS* 4.0 8.9 - - + +
130L GLN* 3.2 42.4 + - - +
133L HIS* 1.3 74.2 - - - +
135L GLY* 1.3 64.0 + - - +
149L GLY* 3.3 3.3 - - - -
150L VAL* 2.8 38.9 + - + +
152L GLN* 3.6 21.3 - - - +
172L SER* 4.3 5.4 - - - -
174L TRP 3.4 22.9 - - - -
175L ASN* 3.4 20.6 - - + -
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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