Contacts of the helix formed by residues 141 - 154 (chain A) in PDB entry 4YVG
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 GLY 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A LEU* 3.8 8.7 - - - +
112A CYS* 3.7 18.7 - - - -
113A GLY 2.9 17.2 + - - -
140A GLY* 1.3 71.4 - - - -
142A GLU* 1.3 58.6 + - - +
144A PRO* 3.4 10.1 - - - +
145A ALA* 2.8 29.8 + - - +
301A SAM 3.3 13.1 + - - -
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Residues in contact with GLU 142 (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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7A SER* 2.6 34.2 + - - +
8A LEU 3.9 6.9 + - - -
9A PHE* 4.1 4.6 + - - +
12A MET* 3.4 30.3 - - + -
13A PHE* 3.7 17.9 - - + -
112A CYS* 3.6 17.7 - - + +
113A GLY 4.1 0.2 - - - +
114A ARG* 2.8 41.4 + - - +
140A GLY 3.3 0.6 - - - -
141A GLY* 1.3 74.0 + - - +
143A LEU* 1.3 63.1 + - - +
145A ALA* 3.2 1.4 + - - +
146A MET* 2.9 36.4 + - + +
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Residues in contact with LEU 143 (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 MET* 4.2 14.8 - - + -
133A ILE* 4.8 2.0 - - + -
138A LEU* 4.2 18.4 - - + -
140A GLY 4.4 1.4 + - - +
142A GLU* 1.3 75.0 - - - +
144A PRO* 1.3 70.9 - - + +
146A MET* 3.3 21.0 + - + +
147A THR* 2.9 29.5 + - - +
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Residues in contact with PRO 144 (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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87A LEU* 3.9 8.7 - - + +
133A ILE* 3.6 24.0 - - + +
138A LEU* 3.6 20.2 - - + -
140A GLY 3.3 19.3 - - - +
141A GLY 3.4 7.2 - - - +
143A LEU* 1.3 94.9 - - + +
145A ALA* 1.4 61.6 + - - +
147A THR* 3.2 3.5 + - - -
148A LEU* 2.9 24.1 + - - +
301A SAM 3.5 40.8 - - + +
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Residues in contact with ALA 145 (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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13A PHE* 4.0 9.9 - - + -
87A LEU* 3.8 14.7 - - + +
110A LEU* 3.8 19.8 - - + +
112A CYS* 3.6 20.2 - - - -
141A GLY 2.8 20.8 + - - +
142A GLU 3.2 5.1 + - - +
144A PRO* 1.4 72.4 - - - +
146A MET* 1.3 59.2 + - - +
148A LEU* 3.2 3.6 + - - +
149A ILE* 2.9 34.6 + - - +
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Residues in contact with MET 146 (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 MET* 3.4 43.3 - - + +
13A PHE* 3.5 30.5 - - + +
15A ALA* 4.0 16.6 - - + -
16A ILE* 3.9 29.0 - - + +
142A GLU* 2.9 29.7 + - + +
143A LEU* 3.8 23.3 - - + +
145A ALA* 1.3 75.5 - - - +
147A THR* 1.3 57.3 + - - +
149A ILE* 3.7 0.9 - - - +
150A ASP* 2.8 32.8 + - - +
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Residues in contact with THR 147 (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 LEU* 4.6 9.6 - - + -
133A ILE* 3.9 30.6 - - + +
143A LEU* 2.9 20.1 + - - +
144A PRO 3.4 5.6 - - - -
146A MET* 1.3 78.1 - - - +
148A LEU* 1.3 56.8 + - - +
150A ASP* 3.7 5.7 - - - +
151A ALA* 3.0 30.3 + - + +
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Residues in contact with LEU 148 (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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85A ILE* 4.5 10.5 - - + -
87A LEU* 4.2 20.4 - - + -
94A LEU* 4.6 15.0 - - + -
102A LEU* 3.9 25.4 - - + -
108A LEU* 4.2 21.3 - - + -
110A LEU* 4.4 20.9 - - + -
131A TRP* 4.6 7.4 - - + -
133A ILE* 5.3 1.6 - - + -
144A PRO 2.9 12.4 + - - +
145A ALA* 3.5 8.5 - - - +
147A THR* 1.3 74.8 - - - +
149A ILE* 1.4 68.5 + - + +
151A ALA* 3.3 5.2 + - - +
152A VAL* 3.0 43.6 + - + +
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Residues in contact with ILE 149 (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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3A ILE* 4.0 21.1 - - + -
5A VAL* 4.3 4.7 - - + -
13A PHE* 4.1 19.3 - - + -
16A ILE* 3.6 32.8 - - + -
22A THR* 5.8 0.7 - - + -
31A LEU* 3.9 31.0 - - + -
33A VAL* 4.7 8.7 - - + -
110A LEU* 3.6 22.2 - - + -
145A ALA 2.9 20.7 + - - +
146A MET 3.7 0.2 - - - +
148A LEU* 1.4 76.5 - - + +
150A ASP* 1.3 64.3 + - - +
152A VAL* 3.3 8.2 - - + +
153A ALA* 2.9 23.0 + - + +
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Residues in contact with ASP 150 (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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16A ILE* 4.8 9.9 - - + +
22A THR* 3.5 31.5 + - + +
146A MET 2.8 21.4 + - - +
147A THR* 3.7 6.3 - - - +
149A ILE* 1.3 73.6 - - - +
151A ALA* 1.3 65.7 + - - +
153A ALA* 3.3 10.4 + - - +
154A ARG* 3.4 23.7 + - - +
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Residues in contact with ALA 151 (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 LEU* 4.8 4.7 - - + -
96A GLN* 5.2 3.5 + - - +
99A VAL* 3.6 37.8 - - + +
147A THR* 3.0 19.9 + - + +
148A LEU* 3.8 5.6 - - - +
150A ASP* 1.3 80.7 + - - +
152A VAL* 1.3 62.0 + - + +
154A ARG* 3.5 21.6 + - - +
155A PHE* 3.7 4.5 - - - -
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Residues in contact with VAL 152 (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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1A MET* 3.7 24.8 - - - +
3A ILE* 4.9 6.1 - - + -
31A LEU* 6.0 0.4 - - + -
99A VAL* 4.0 19.3 - - + +
102A LEU* 3.9 30.7 - - + +
103A ALA* 4.1 12.5 - - + +
108A LEU* 5.2 1.8 - - + -
148A LEU* 3.0 25.9 + - + +
149A ILE* 3.3 17.5 - - + +
151A ALA* 1.3 74.0 - - + +
153A ALA* 1.3 69.7 + - + +
154A ARG 3.1 2.2 - - - -
155A PHE* 3.0 21.4 + - - +
156A ILE* 3.8 6.6 + - - +
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Residues in contact with ALA 153 (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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22A THR* 4.2 15.9 - - + -
25A ALA* 5.5 0.9 - - + -
31A LEU* 4.2 23.3 - - + -
149A ILE 2.9 17.6 + - - +
150A ASP 3.7 5.6 - - - +
152A VAL* 1.3 80.0 - - + +
154A ARG* 1.3 62.2 + - + +
156A ILE* 3.0 26.6 + - + +
159A VAL* 3.3 25.3 - - + +
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Residues in contact with ARG 154 (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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21A VAL* 5.8 2.2 - - + -
22A THR* 6.4 0.9 - - + -
96A GLN* 4.1 21.6 + - - +
150A ASP* 3.4 25.3 + - - +
151A ALA* 3.6 12.5 + - - +
152A VAL 3.1 0.2 - - - -
153A ALA* 1.3 79.0 - - + +
155A PHE* 1.3 66.0 + - + +
156A ILE 3.7 3.8 + - - +
159A VAL* 4.4 2.9 - - + -
160A LEU* 3.7 54.4 - - + +
169A ASP* 3.0 32.1 + - - -
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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