Contacts of the helix formed by residues 144 - 155 (chain L) in PDB entry 5AYZ
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 PHE 144 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141K THR* 3.6 19.3 - - + -
142K PRO* 3.6 43.1 - - + +
18L LEU* 6.4 0.7 - - - -
22L TRP* 3.7 21.5 - + - -
107L THR* 4.0 13.9 - - + -
110L ARG* 4.0 19.7 - - + -
141L THR* 2.9 23.7 + - + +
142L PRO 4.6 0.7 - - - +
143L GLY* 1.3 77.4 - - - +
145L ARG* 1.3 65.3 - - - +
146L LEU 3.2 2.7 - - - -
147L VAL* 3.1 51.4 + - + +
148L GLU* 3.2 29.9 + - + +
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Residues in contact with ARG 145 (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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25K GLU* 3.1 32.1 + - + +
26K ASP* 2.2 53.4 + - - +
102K ARG* 5.3 0.2 - - - +
103K VAL* 6.1 0.8 - - - +
106K ASN* 4.6 4.2 - - - +
138L ARG* 3.5 26.1 + - - +
140L THR* 2.7 53.0 + - - +
141L THR 3.7 2.2 + - - -
144L PHE* 1.3 76.3 - - - +
146L LEU* 1.3 59.3 + - - +
148L GLU 3.1 0.6 + - - +
149L LYS* 2.8 47.8 + - + +
162L TYR* 3.0 39.1 + - + +
163L ASP* 3.9 4.9 - - - +
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Residues in contact with LEU 146 (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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29H GLY* 4.3 12.6 - - - +
30H LEU* 3.7 29.6 - - + -
25K GLU* 4.6 1.6 + - - -
10L LEU* 3.8 22.0 - - + -
11L PRO* 4.9 4.7 - - + -
14L THR* 4.2 19.7 - - + -
15L LEU* 4.8 6.7 - - + +
18L LEU* 3.8 30.3 - - + -
59L PHE* 3.8 10.0 - - + -
144L PHE 3.2 0.6 - - - -
145L ARG* 1.3 78.0 - - - +
147L VAL* 1.3 62.2 + - - +
149L LYS* 4.6 0.2 - - - +
150L TYR* 3.2 24.9 + - - +
162L TYR* 3.3 25.2 + - + +
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Residues in contact with VAL 147 (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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18L LEU* 5.4 0.9 - - + -
22L TRP* 3.4 34.5 - - + -
59L PHE* 3.6 23.1 - - + -
107L THR* 3.9 8.3 - - + +
111L CYS* 3.7 33.7 - - + -
144L PHE* 3.1 41.7 + - + +
146L LEU* 1.3 79.5 - - + +
148L GLU* 1.3 57.4 + - + +
150L TYR* 3.6 2.1 - - - +
151L GLY* 2.9 24.1 + - - -
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Residues in contact with GLU 148 (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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110K ARG* 4.4 0.2 + - - -
141K THR* 5.3 0.5 - - - +
110L ARG* 5.6 2.6 - - - +
111L CYS* 5.9 0.7 - - - +
114L ILE* 3.6 36.7 - - + +
140L THR* 3.1 18.2 - - + +
141L THR* 2.8 46.4 + - - +
144L PHE* 3.4 32.4 - - + +
145L ARG 3.1 5.7 + - - +
147L VAL* 1.3 74.5 - - - +
149L LYS* 1.3 66.2 + - - +
151L GLY* 3.4 0.6 + - - +
152L LEU* 3.1 26.8 + - - +
273L THR* 4.4 17.4 - - + +
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Residues in contact with LYS 149 (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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30H LEU* 4.9 3.6 - - + -
137L THR* 2.6 35.3 + - - +
138L ARG* 4.2 1.3 - - - +
140L THR* 4.2 4.9 - - + -
145L ARG* 2.8 51.9 + - + +
146L LEU 4.6 0.4 - - - +
148L GLU* 1.3 69.9 - - - +
150L TYR* 1.3 65.8 + - - +
152L LEU* 3.3 14.2 + - + +
153L LEU* 3.2 24.9 + - - +
159L SER* 2.8 41.1 + - - +
160L HIS* 4.4 0.6 - - - +
161L ARG 3.1 23.1 + - - +
162L TYR* 3.9 24.9 - - + -
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Residues in contact with TYR 150 (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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30H LEU* 5.3 6.6 - - + +
3L ALA 4.5 0.3 + - - -
6L LEU* 3.8 37.8 - - + +
7L ALA* 4.0 7.3 + - - +
9L LEU* 5.5 2.7 - - + -
10L LEU* 4.0 22.0 - - + -
56L GLY* 3.9 11.7 - - - -
58L PRO* 3.5 16.4 - - + +
59L PHE* 3.7 21.3 - + + -
77L GLU* 2.5 39.2 + - - +
111L CYS* 3.9 7.4 - - - -
146L LEU 3.2 19.9 + - - +
147L VAL 3.6 1.1 - - - +
149L LYS* 1.3 79.0 - - - +
151L GLY* 1.3 63.3 + - - +
153L LEU* 3.0 14.6 + - + +
154L VAL* 3.0 35.0 + - + +
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Residues in contact with GLY 151 (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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111L CYS* 3.9 25.8 - - - -
114L ILE* 4.0 9.6 - - - -
115L ALA* 3.3 13.7 - - - +
147L VAL 2.9 16.8 + - - -
148L GLU 3.4 2.9 + - - -
149L LYS 3.3 0.2 - - - -
150L TYR* 1.3 74.5 - - - +
152L LEU* 1.3 64.7 + - - +
154L VAL* 3.2 3.5 + - - -
155L GLY 3.2 17.5 + - - -
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Residues in contact with LEU 152 (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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114L ILE* 3.8 12.9 - - + +
118L ALA* 3.9 9.6 - - + +
136L GLY* 3.7 26.7 - - - +
137L THR 4.7 0.9 - - - +
148L GLU 3.1 20.0 + - - +
149L LYS* 3.4 17.3 - - + +
150L TYR 3.3 0.2 - - - -
151L GLY* 1.3 76.9 - - - +
153L LEU* 1.3 62.5 + - - +
155L GLY* 3.4 5.5 + - - -
156L GLY 3.4 0.2 + - - -
157L ALA* 3.0 34.3 + - + +
158L ALA 4.5 3.6 - - - +
159L SER* 4.1 18.6 - - - +
272L LEU* 3.8 39.7 - - + -
273L THR* 4.4 11.4 - - + -
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Residues in contact with LEU 153 (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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191G ALA 6.1 0.7 - - - +
30H LEU* 4.3 15.0 - - + -
32H TYR* 5.7 2.9 - - + -
6L LEU* 3.8 26.0 - - + +
9L LEU* 3.5 32.5 - - + -
149L LYS 3.2 12.5 + - - +
150L TYR* 3.0 14.1 + - + +
152L LEU* 1.3 76.0 - - - +
154L VAL* 1.3 67.9 + - - +
156L GLY* 2.9 15.4 + - - -
157L ALA 3.5 16.8 - - - +
158L ALA* 4.5 2.0 - - - -
159L SER* 3.9 20.2 - - - +
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Residues in contact with VAL 154 (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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3L ALA* 4.1 13.5 - - + +
6L LEU* 4.0 14.4 - - + -
53L VAL* 4.2 8.1 - - + +
54L LEU 3.7 13.9 - - - +
55L ALA* 3.4 30.5 - - + -
77L GLU* 4.0 6.1 - - + +
78L GLY* 3.8 16.6 - - - +
150L TYR* 3.0 51.9 + - + +
151L GLY 3.2 3.6 + - - +
153L LEU* 1.3 75.2 - - - +
155L GLY* 1.3 57.4 + - - +
156L GLY 3.3 4.2 + - - -
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Residues in contact with GLY 155 (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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53L VAL* 4.8 3.6 - - - -
115L ALA* 3.5 25.4 - - - +
118L ALA* 3.5 4.6 - - - +
119L ALA* 3.2 31.5 + - - +
122L VAL* 4.2 3.1 - - - +
151L GLY 3.2 11.6 + - - -
152L LEU 3.4 3.3 + - - -
153L LEU 3.2 0.2 - - - -
154L VAL* 1.3 75.2 - - - +
156L GLY* 1.3 58.7 + - - +
157L ALA 3.4 2.9 - - - -
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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