Contacts of the strand formed by residues 68 - 76 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A GLY* 1.3 78.6 - - - +
69A GLN* 1.3 61.7 + - - +
70A ALA 4.2 0.2 - - - -
112A ALA 4.0 0.3 - - - +
113A PHE* 3.4 6.8 - - - +
114A PHE* 2.7 50.5 + - + +
115A THR 4.0 0.6 + - - -
116A ASP* 3.7 33.0 - - - +
117A MSE 3.8 16.2 - - + +
120A PHE* 3.7 22.2 - - + -
141A PHE* 3.7 27.6 - - + -
142A VAL 5.8 0.2 - - - +
1011A CL 4.5 2.5 - - + -
117D MSE 3.8 39.5 - - + -
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Residues in contact with GLN 69 (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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67A GLY 4.0 2.4 + - - -
68A LEU* 1.3 75.6 - - - +
70A ALA* 1.3 61.9 + - - +
71A PHE* 4.2 3.9 - - + -
111A GLN* 2.8 40.4 - - + +
112A ALA 3.5 8.1 - - - +
113A PHE* 3.3 35.0 - - + -
141A PHE* 3.3 8.6 - - - +
142A VAL* 3.0 54.4 + - + +
145A GLU* 4.9 3.1 - - - +
148A HIS* 6.1 0.6 + - - -
100B PHE* 3.7 26.7 - - - -
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Residues in contact with ALA 70 (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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68A LEU* 4.2 0.4 - - + -
69A GLN* 1.3 75.1 - - - +
71A PHE* 1.3 65.4 + - - +
72A ILE* 4.0 8.2 - - + +
110A LEU 3.5 0.7 - - - +
111A GLN* 3.4 6.8 - - - +
112A ALA* 2.9 35.9 + - + +
114A PHE* 4.2 5.8 - - + -
120A PHE* 3.6 34.1 - - + -
139A SER* 5.1 0.2 - - - -
140A SER 3.4 5.8 - - - +
141A PHE* 3.7 13.2 - - + -
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Residues in contact with PHE 71 (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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69A GLN* 4.3 5.2 - - - -
70A ALA* 1.3 73.6 - - - +
72A ILE* 1.3 61.0 - - - +
73A ARG* 3.9 3.7 + - + +
109A LEU* 4.3 19.5 - - + -
110A LEU 3.3 11.0 - - - -
111A GLN* 3.2 37.0 - - + -
138A GLN 4.1 0.2 - - - +
139A SER* 3.2 3.3 - - - -
140A SER* 2.8 41.0 + - - +
142A VAL* 3.7 26.0 - - + -
71B PHE* 4.9 2.7 - + - -
100B PHE* 3.7 22.7 - + - -
102B LEU* 3.7 31.4 - - + -
109B LEU* 3.5 26.7 - - + -
111B GLN* 4.0 6.5 - - - -
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Residues in contact with ILE 72 (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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70A ALA* 4.1 11.4 - - + -
71A PHE* 1.3 74.2 - - - +
73A ARG* 1.3 59.9 + - - +
74A VAL* 3.6 11.1 + - + -
108A TYR 3.4 2.8 - - - +
109A LEU* 3.4 5.8 - - - +
110A LEU* 2.8 54.4 + - + +
112A ALA* 4.3 16.8 - - + -
120A PHE* 3.7 23.1 - - + -
123A PHE* 3.9 23.8 - - + -
128A LEU* 3.7 24.5 - - + -
137A ALA* 4.0 8.3 - - + -
138A GLN 3.7 2.2 - - - +
139A SER* 3.4 20.4 - - - +
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Residues in contact with ARG 73 (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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71A PHE* 5.0 2.9 - - + +
72A ILE* 1.3 70.1 - - - +
74A VAL* 1.3 60.2 + - - +
75A SER 4.1 0.5 + - - -
105A GLU* 4.4 8.1 + - - -
106A THR* 3.4 34.7 + - + +
109A LEU* 3.9 15.7 - - + +
137A ALA* 3.3 2.9 - - - -
138A GLN* 2.7 67.3 + - + +
139A SER* 5.8 0.4 - - - -
140A SER* 5.9 8.4 - - - -
73B ARG* 3.1 46.4 - - - +
102B LEU* 6.1 2.2 - - - +
105B GLU* 3.7 20.0 + - - +
106B THR* 3.7 16.8 + - - -
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Residues in contact with VAL 74 (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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72A ILE* 3.9 18.4 - - + -
73A ARG* 1.3 75.9 - - - +
75A SER* 1.3 72.3 + - - +
76A ILE* 4.4 2.7 - - + +
86A PHE* 4.0 17.7 - - + -
106A THR* 3.9 1.1 - - - +
107A ASP* 3.3 9.9 + - - +
108A TYR* 2.8 42.9 + - + +
110A LEU* 3.9 21.3 - - + -
128A LEU* 4.1 15.9 - - + -
134A VAL* 4.1 15.7 - - + -
136A ASP 3.5 9.0 - - - +
137A ALA* 4.3 3.6 - - + -
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Residues in contact with SER 75 (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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73A ARG 4.1 0.6 + - - -
74A VAL* 1.3 77.1 - - - +
76A ILE* 1.3 53.9 + - - +
105A GLU 5.8 1.5 + - - -
107A ASP* 3.4 15.3 + - - -
134A VAL 3.8 0.9 - - - -
135A GLN* 2.8 53.1 + - - -
136A ASP* 2.7 29.6 + - - +
136G ASP* 4.7 6.4 + - - -
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Residues in contact with ILE 76 (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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74A VAL* 4.0 2.3 + - + -
75A SER* 1.3 74.4 + - - +
77A ARG* 1.3 72.1 + - - +
78A LYS* 3.7 1.3 + - - -
82A ALA* 3.9 13.2 - - + +
83A ARG* 4.1 37.2 - - + +
86A PHE* 3.5 45.5 - - + -
107A ASP* 3.0 20.7 + - - +
108A TYR* 3.9 13.7 - - + -
133A GLY 3.3 18.2 - - - +
134A VAL* 4.9 2.2 - - + -
135A GLN* 3.4 13.6 - - - +
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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