Contacts of the strand formed by residues 139 - 144 (chain D) in PDB entry 4AY1
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 139 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D ILE 4.0 2.2 + - - -
98D LEU* 3.3 11.4 - - - +
99D LEU 3.0 22.7 + - - -
132D LEU* 3.7 21.2 - - - +
137D PHE* 3.4 4.5 + - - +
138D ASP* 1.3 79.1 - - - +
140D LEU* 1.3 59.3 + - - -
178D LEU* 4.1 2.5 - - - +
179D LEU* 3.1 18.4 - - - -
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 4.2 2.8 - - - +
99D LEU* 3.4 22.7 - - + +
101D ILE* 3.7 32.5 - - + -
124D PHE* 5.0 2.9 - - + -
128D ILE* 4.1 19.3 - - + -
132D LEU* 4.0 6.7 - - + +
139D GLY* 1.3 73.7 - - - -
141D ASP* 1.3 62.7 + - - +
142D VAL* 3.6 26.5 - - + -
162D LEU* 3.9 28.0 - - + -
166D PHE* 4.0 15.9 - - + -
179D LEU 2.9 6.3 + - - +
180D LEU* 3.4 7.6 - - + +
181D THR* 3.0 24.8 + - - +
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Residues in contact with ASP 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D TYR* 2.7 23.8 + - - -
60D ILE* 4.0 13.8 - - + +
98D LEU* 4.5 2.2 - - + +
99D LEU 2.7 15.8 + - - +
100D SER* 2.8 20.2 + - - +
101D ILE 3.0 24.8 + - - -
140D LEU* 1.3 73.5 - - - +
142D VAL* 1.3 59.9 + - - +
143D SER* 2.6 24.4 + - - -
181D THR* 2.7 25.4 + - - +
182D ALA 3.5 3.6 + - - -
183D GLY 3.4 14.0 + - - -
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Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ILE* 3.8 5.6 - - + +
111D PHE* 4.3 22.9 - - + -
124D PHE* 6.2 1.3 - - + -
140D LEU* 3.6 29.4 - - + -
141D ASP* 1.3 71.7 - - - +
143D SER* 1.3 61.8 + - - +
144D TRP* 3.7 8.0 + - + +
155D PHE* 4.2 21.0 - - + -
158D LEU* 4.8 7.0 - - + -
159D ILE* 4.0 16.6 - - + -
162D LEU* 3.9 18.2 - - + -
180D LEU* 4.3 4.0 - - + -
181D THR 2.8 11.6 + - - +
182D ALA* 3.1 24.3 - - - +
183D GLY 3.3 1.7 + - - +
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Residues in contact with SER 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D TYR* 3.4 4.9 + - - -
63D PHE* 4.6 4.9 - - - -
100D SER* 3.8 8.7 + - - -
101D ILE 3.0 13.1 + - - -
102D GLY* 3.4 1.2 - - - -
103D GLY* 2.8 31.8 + - - -
141D ASP* 2.6 26.4 + - - -
142D VAL* 1.3 68.7 - - - +
144D TRP* 1.3 61.7 + - - +
145D ILE* 3.3 11.1 + - - +
183D GLY* 3.2 25.8 + - - -
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Residues in contact with TRP 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D GLY 4.1 1.6 - - - -
108D SER* 2.9 27.2 + - - +
111D PHE* 3.5 60.6 - + + -
112D HIS* 5.0 0.2 - - - -
115D VAL* 4.0 17.7 - - + -
142D VAL* 3.6 4.6 + - + -
143D SER* 1.3 73.2 - - - +
145D ILE* 1.3 66.8 + - - +
146D TYR* 3.3 34.0 + - - -
147D PRO* 3.5 15.2 - - + +
151D GLU* 3.5 42.0 - - + -
154D HIS* 4.2 8.1 - - + -
155D PHE* 3.7 47.9 - + + -
158D LEU* 4.3 6.7 - - + -
183D GLY 4.2 5.6 + - - +
184D VAL* 6.0 0.2 - - - -
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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