Contacts of the strand formed by residues 68 - 76 (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 LEU 68 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A MSE 3.3 34.3 - - + -
1011A CL 4.7 0.2 - - + -
66D LEU 3.2 0.2 - - - -
67D GLY* 1.3 77.4 - - - +
69D GLN* 1.3 60.9 - - - +
70D ALA 4.1 0.2 + - - -
112D ALA 4.0 0.3 - - - +
113D PHE* 3.4 7.3 - - - -
114D PHE* 2.8 49.2 + - + +
115D THR 3.9 0.4 + - - -
116D ASP* 3.4 35.4 - - - +
117D MSE 3.5 21.3 - - + +
120D PHE* 3.7 16.8 - - + -
141D PHE* 3.5 30.3 - - + -
142D VAL 5.9 0.4 - - - +
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Residues in contact with GLN 69 (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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901A GOL 5.6 1.8 + - - +
100C PHE* 3.6 25.0 - - - -
61D PRO* 5.6 0.2 - - - +
67D GLY 4.0 2.7 + - - +
68D LEU* 1.3 74.4 - - - +
70D ALA* 1.3 63.9 + - - +
71D PHE* 4.5 2.4 - - + -
111D GLN* 2.7 34.2 - - + +
112D ALA 3.5 7.4 - - - +
113D PHE* 3.3 34.2 - - + -
141D PHE* 3.2 7.2 - - - +
142D VAL* 3.0 61.2 + - + +
145D GLU* 4.6 5.4 + - - +
148D HIS* 5.9 1.2 + - - -
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Residues in contact with ALA 70 (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* 4.1 1.0 - - + -
69D GLN* 1.3 74.5 - - - +
71D PHE* 1.3 65.0 + - - +
72D ILE* 4.0 9.2 - - + -
110D LEU 3.7 0.3 - - - +
111D GLN* 3.4 6.4 - - - +
112D ALA* 2.8 36.2 + - - +
114D PHE* 4.3 6.7 - - + -
120D PHE* 3.7 32.5 - - + -
139D SER* 5.0 0.2 - - - -
140D SER 3.5 5.4 - - - +
141D PHE* 3.7 14.6 - - + -
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Residues in contact with PHE 71 (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* 4.9 9.0 - + - -
100C PHE* 3.6 24.9 - + - -
102C LEU* 3.8 27.1 - - + -
109C LEU* 3.7 26.0 - - + -
111C GLN* 5.8 0.2 - - - -
69D GLN* 4.5 1.6 - - + -
70D ALA* 1.3 73.0 - - - +
72D ILE* 1.3 62.0 + - - +
73D ARG* 4.0 3.5 + - + +
109D LEU* 4.2 18.8 - - + -
110D LEU 3.3 9.6 - - - -
111D GLN* 3.5 39.7 - - + -
138D GLN 4.0 0.2 - - - +
139D SER* 3.4 1.9 - - - -
140D SER* 2.9 40.0 + - - +
142D VAL* 3.8 24.9 - - + -
903D GOL 5.5 1.6 - - - +
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Residues in contact with ILE 72 (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* 4.1 5.2 - - + -
71D PHE* 1.3 74.8 - - - +
73D ARG* 1.3 62.0 + - - +
74D VAL* 3.6 10.1 + - + -
108D TYR 3.4 4.9 - - - +
109D LEU* 3.5 2.6 - - - -
110D LEU* 2.9 54.6 + - + +
112D ALA* 4.1 23.8 - - + -
120D PHE* 4.0 23.3 - - + -
123D PHE* 4.2 19.1 - - + -
128D LEU* 3.7 25.1 - - + -
137D ALA* 3.9 8.3 - - + -
138D GLN 3.7 2.7 - - - +
139D SER* 3.4 22.4 - - - +
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Residues in contact with ARG 73 (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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73C ARG* 4.5 6.2 - - - +
102C LEU* 6.0 1.4 - - - +
105C GLU* 4.2 19.8 + - - +
106C THR* 3.5 26.9 + - - +
71D PHE* 4.9 2.9 - - + +
72D ILE* 1.3 71.6 - - - +
74D VAL* 1.3 62.3 + - - +
75D SER* 4.0 1.4 + - - -
106D THR* 3.5 17.5 - - + +
108D TYR 3.5 4.7 - - - -
109D LEU* 4.0 5.4 - - + -
136D ASP 3.9 0.2 - - - +
137D ALA* 3.2 3.3 - - - -
138D GLN* 2.8 69.1 + - + +
140D SER* 5.4 10.5 + - - -
903D GOL 2.7 48.9 + - - +
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Residues in contact with VAL 74 (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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72D ILE* 3.9 17.9 - - + +
73D ARG* 1.3 75.2 - - - +
75D SER* 1.3 71.6 + - - +
76D ILE* 4.6 2.7 - - + +
86D PHE* 3.8 21.1 - - + -
106D THR* 4.1 0.8 - - - +
107D ASP* 3.3 9.9 + - - +
108D TYR* 2.8 45.2 + - + +
110D LEU* 3.7 28.3 - - + -
128D LEU* 4.2 10.3 - - + -
134D VAL* 4.2 16.8 - - + -
136D ASP 3.5 7.9 - - - +
137D ALA* 4.3 2.9 - - + -
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Residues in contact with SER 75 (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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73D ARG 4.0 2.1 + - - -
74D VAL* 1.3 76.7 - - - +
76D ILE* 1.3 55.8 + - - +
78D LYS* 5.2 2.2 - - - -
105D GLU 5.1 5.5 + - - -
106D THR* 5.7 1.2 - - - -
107D ASP* 3.4 11.9 + - - -
134D VAL 3.8 0.7 - - - -
135D GLN* 2.8 36.7 + - - +
136D ASP* 2.7 31.1 + - - +
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Residues in contact with ILE 76 (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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74D VAL* 3.9 2.3 + - + -
75D SER* 1.3 73.7 - - - +
77D ARG* 1.3 70.4 + - - +
78D LYS* 3.0 32.5 + - + +
82D ALA 3.7 4.3 - - - +
83D ARG* 4.1 41.5 - - + +
86D PHE* 3.5 44.2 - - + -
107D ASP* 2.8 23.2 + - + +
108D TYR* 3.9 14.1 - - + -
133D GLY 3.1 21.5 - - - +
134D VAL* 4.8 2.0 - - + +
135D GLN* 3.9 5.4 - - - +
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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