Contacts of the helix formed by residues 133 - 142 (chain A) in PDB entry 2YF3
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 ASP 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A GLU* 2.5 23.7 + - - +
131A PRO 3.3 4.0 + - - +
132A ALA* 1.3 69.9 - - - +
134A VAL* 1.3 62.2 + - - +
135A ARG* 3.8 8.5 + - - +
136A GLY* 3.1 25.1 + - - -
137A VAL* 3.2 21.5 + - - +
140A ARG* 4.7 3.2 + - - +
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Residues in contact with VAL 134 (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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101A VAL* 3.8 34.3 - - + +
104A GLU* 4.5 6.7 - - + -
105A VAL* 4.3 12.1 - - + -
132A ALA* 3.6 9.7 + - + -
133A ASP* 1.3 73.0 + - - +
135A ARG* 1.3 66.3 + - - +
137A VAL* 3.1 6.9 + - + +
138A ILE* 2.9 28.0 + - + +
74B ALA* 3.6 22.0 - - + +
77B ALA* 4.1 7.2 - - + -
78B HIS* 3.9 37.2 + - + +
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Residues in contact with ARG 135 (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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133A ASP* 3.4 7.6 - - - +
134A VAL* 1.3 76.6 - - - +
136A GLY* 1.3 56.2 - - - +
138A ILE* 3.4 2.8 + - - +
139A GLU* 3.0 28.4 + - - +
71B GLY* 3.2 31.3 + - - +
72B ASP* 4.7 2.6 + - - +
74B ALA* 3.5 19.4 - - + +
75B PRO* 3.6 26.7 - - - +
129C TRP* 4.0 24.7 + - - -
130C ARG* 5.0 13.7 - - - +
131C PRO* 3.7 36.9 - - - +
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Residues in contact with GLY 136 (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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133A ASP* 3.1 27.9 + - - -
134A VAL 3.2 0.4 - - - -
135A ARG* 1.3 76.2 - - - +
137A VAL* 1.3 55.3 + - - +
139A GLU* 3.4 7.9 + - - +
140A ARG* 3.0 39.9 + - - +
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Residues in contact with VAL 137 (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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100A ALA* 3.8 25.1 - - + +
101A VAL* 3.9 23.6 - - + -
104A GLU* 3.6 27.4 - - + -
133A ASP 3.2 14.6 + - - +
134A VAL* 3.1 11.4 + - + +
136A GLY* 1.3 75.1 - - - +
138A ILE* 1.3 62.7 + - - +
140A ARG* 3.3 31.3 + - - +
141A LEU* 3.0 37.7 + - + +
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Residues in contact with ILE 138 (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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29A PRO* 4.0 11.1 - - + +
96A ILE* 3.7 41.3 - - + -
101A VAL* 4.2 13.7 - - + -
134A VAL* 2.9 20.0 + - + +
135A ARG 3.8 7.4 - - - +
137A VAL* 1.3 71.6 - - - +
139A GLU* 1.3 63.6 + - - +
141A LEU* 3.4 9.8 + - + +
142A GLN* 3.2 35.4 + - - +
70B ALA 3.6 25.8 - - - +
71B GLY* 4.3 4.7 - - - -
73B LEU* 5.6 0.2 - - + -
74B ALA* 4.1 24.7 - - + +
77B ALA* 4.3 3.6 - - + -
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Residues in contact with GLU 139 (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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135A ARG 3.0 14.5 + - - +
136A GLY* 3.5 11.2 - - - +
138A ILE* 1.3 76.9 - - - +
140A ARG* 1.3 59.8 + - + +
142A GLN* 3.3 25.7 + - - +
143A HIS* 2.6 56.7 + - + +
130C ARG* 5.2 8.1 + - - -
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Residues in contact with ARG 140 (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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100A ALA* 5.7 3.4 + - - +
104A GLU* 5.2 5.5 + - - -
133A ASP* 4.7 4.2 + - - +
136A GLY* 3.0 15.6 + - - +
137A VAL* 3.3 54.2 + - - +
139A GLU* 1.3 76.6 - - + +
141A LEU* 1.3 58.7 + - + +
143A HIS* 2.9 9.2 + - - +
144A ALA* 2.9 32.1 + - + +
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Residues in contact with LEU 141 (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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27A GLU 5.4 1.5 - - - +
28A ARG* 2.9 29.6 + - - +
29A PRO* 3.9 14.8 - - + -
95A GLY 5.5 0.2 - - - +
96A ILE* 4.2 14.1 - - + -
97A ASP* 3.8 47.1 - - + +
100A ALA* 4.1 11.7 - - + -
137A VAL* 3.0 36.2 + - + +
138A ILE* 3.7 10.8 - - + +
140A ARG* 1.3 76.8 - - + +
142A GLN* 1.3 57.1 + - - +
144A ALA* 3.8 9.6 + - + +
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Residues in contact with GLN 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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28A ARG* 3.4 18.8 + - + +
29A PRO* 4.1 19.1 - - + +
138A ILE* 3.2 29.6 + - - +
139A GLU* 3.4 29.9 + - - +
140A ARG 3.2 0.4 - - - -
141A LEU* 1.3 75.9 - - - +
143A HIS* 1.3 72.5 + - + +
70B ALA* 3.5 24.9 - - + +
71B GLY* 4.5 5.3 - - - +
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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