Contacts of the strand formed by residues 108 - 114 (chain D) in PDB entry 2P5V
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 TYR 108 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C ILE* 3.7 21.7 - - + +
72D ILE 3.4 1.4 - - - +
74D VAL* 2.8 44.5 + - + +
76D ILE* 3.9 30.5 - - + -
83D ARG* 3.1 40.5 + - - +
86D PHE* 4.0 20.0 - + + -
87D ALA* 6.0 0.4 - - + -
99D CYS* 3.8 15.5 - - - -
100D PHE 3.2 4.9 - - - +
101D ALA* 3.8 24.9 - - + -
106D THR* 3.1 8.6 - - - +
107D ASP* 1.3 84.8 - - + +
109D LEU* 1.3 58.1 - - - +
110D LEU* 3.8 15.7 - - + -
1014D CL 3.0 20.4 - - + +
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Residues in contact with LEU 109 (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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71C PHE* 3.3 44.9 - - + -
109C LEU* 4.3 10.3 - - + -
71D PHE* 4.2 21.1 - - + -
72D ILE 3.8 13.9 - - - +
73D ARG* 4.0 7.9 - - + -
98D SER* 4.0 0.3 + - - +
99D CYS* 3.3 2.8 - - - -
100D PHE* 2.9 36.9 + - + +
102D LEU* 3.7 18.3 - - + +
106D THR* 4.0 0.8 - - - +
108D TYR* 1.3 73.0 - - - +
110D LEU* 1.3 64.4 + - - +
903D GOL 3.7 36.1 - - - +
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Residues in contact with LEU 110 (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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70D ALA 3.7 0.3 - - - +
71D PHE* 3.3 8.1 - - - +
72D ILE* 2.9 50.5 + - + +
74D VAL* 3.7 31.4 - - + -
86D PHE* 4.2 13.7 - - + -
90D VAL* 4.3 5.6 - - + -
93D TRP* 4.8 0.9 - - + -
96D VAL* 3.9 32.1 - - + -
98D SER* 3.2 5.8 - - - +
99D CYS* 3.6 24.0 - - - -
108D TYR* 3.8 10.3 - - + +
109D LEU* 1.3 80.8 - - - +
111D GLN* 1.3 60.7 + - - +
112D ALA 4.2 0.4 - - - -
123D PHE* 5.4 0.9 - - + -
128D LEU* 4.6 9.6 - - + -
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Residues in contact with GLN 111 (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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71C PHE* 5.7 0.5 - - - -
100C PHE* 4.4 8.4 - - - -
111C GLN* 4.4 12.8 - - - +
69D GLN* 2.7 32.0 - - + +
70D ALA 3.4 6.1 - - - +
71D PHE* 3.5 35.0 - - + -
96D VAL* 3.5 3.5 - - - -
97D LEU* 2.7 39.7 + - + +
98D SER* 2.9 28.5 + - - +
110D LEU* 1.3 72.6 - - - +
112D ALA* 1.3 57.1 + - - +
113D PHE* 4.3 10.1 - - + -
148D HIS* 5.1 8.5 + - - -
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Residues in contact with ALA 112 (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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68D LEU 4.0 0.2 - - - +
69D GLN* 3.5 5.2 - - - +
70D ALA* 2.8 32.1 + - + +
72D ILE* 4.1 17.3 - - + -
95D GLU 3.0 19.1 - - - +
96D VAL* 4.0 7.6 - - + -
97D LEU 4.4 0.4 - - - +
111D GLN* 1.3 76.5 - - - +
113D PHE* 1.3 65.4 + - - +
114D PHE* 3.4 26.2 - - + -
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Residues in contact with PHE 113 (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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152C LEU* 3.8 10.8 - - + -
153C PRO* 3.9 13.3 - - + +
61D PRO* 3.6 40.6 - - + -
66D LEU* 4.0 27.8 - - + +
68D LEU 3.4 11.2 - - - -
69D GLN* 3.3 46.7 - - + -
95D GLU* 2.9 20.6 + - - +
97D LEU* 3.7 34.5 - - + -
111D GLN* 4.3 7.9 - - + -
112D ALA* 1.3 76.7 - - - +
114D PHE* 1.3 72.8 + - - +
145D GLU* 6.2 0.2 - - - -
148D HIS* 6.3 3.4 - + - -
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Residues in contact with PHE 114 (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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66D LEU* 3.4 10.5 - - - +
67D GLY 3.3 5.0 + - - -
68D LEU* 2.8 41.4 + - + +
70D ALA* 4.3 3.8 - - + -
95D GLU* 3.8 20.6 - - + -
112D ALA* 3.4 33.9 - - + -
113D PHE* 1.3 86.3 - - - +
115D THR* 1.3 60.7 + - - +
116D ASP 3.9 15.3 - - - +
119D ALA* 4.0 7.9 - - + -
120D PHE* 3.4 41.3 - + + +
123D PHE* 3.5 45.5 - + + -
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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