Contacts of the strand formed by residues 68 - 76 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E MSE 3.8 32.3 - - + -
1020E CL 4.4 2.9 - - + -
66H LEU 3.2 0.4 - - - -
67H GLY* 1.3 78.8 - - - +
69H GLN* 1.3 60.7 + - - +
70H ALA 4.0 0.2 + - - -
112H ALA 3.9 0.3 - - - +
113H PHE* 3.5 7.0 - - - -
114H PHE* 2.9 46.3 + - + +
115H THR 4.2 0.4 + - - +
116H ASP* 3.2 38.4 - - - +
117H MSE 3.4 17.3 - - + +
120H PHE* 3.8 15.5 - - + -
141H PHE* 3.7 33.7 - - + -
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Residues in contact with GLN 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G PHE* 3.5 26.9 - - - -
61H PRO* 5.3 1.2 - - - +
67H GLY 4.0 3.0 + - - -
68H LEU* 1.3 73.5 - - - +
70H ALA* 1.3 65.3 + - - +
71H PHE* 4.1 3.2 - - + -
111H GLN* 3.4 31.8 - - + +
112H ALA 3.5 6.3 - - - +
113H PHE* 3.2 40.1 - - + -
141H PHE* 3.3 7.6 - - - +
142H VAL* 3.0 54.3 + - + +
145H GLU* 4.7 5.0 - - - +
148H HIS* 6.2 0.2 - - - -
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Residues in contact with ALA 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H LEU* 4.0 0.8 + - + -
69H GLN* 1.3 74.3 - - - +
71H PHE* 1.3 64.8 + - - +
72H ILE* 4.0 9.4 - - + -
110H LEU 3.7 0.9 - - - +
111H GLN* 3.4 5.7 - - - +
112H ALA* 2.8 40.4 + - - +
114H PHE* 4.3 7.2 - - + -
120H PHE* 3.7 32.8 - - + -
139H SER* 5.0 0.2 - - - -
140H SER 3.4 5.4 - - - +
141H PHE* 3.8 13.0 - - + -
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Residues in contact with PHE 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G PHE* 5.0 4.5 - + - -
100G PHE* 3.5 34.8 - + - -
102G LEU* 3.7 29.8 - - + -
109G LEU* 3.6 27.4 - - + -
111G GLN* 5.3 0.9 - - - -
69H GLN* 4.1 4.9 - - - -
70H ALA* 1.3 75.2 - - - +
72H ILE* 1.3 61.0 + - - +
73H ARG* 4.0 5.0 + - + +
109H LEU* 4.4 22.4 - - + -
110H LEU 3.3 7.0 - - - +
111H GLN* 3.4 39.7 - - + -
138H GLN 4.0 0.2 - - - +
139H SER* 3.3 2.8 - - - -
140H SER* 2.8 39.0 + - - +
142H VAL* 3.8 17.7 - - + -
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Residues in contact with ILE 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H ALA* 4.1 10.5 - - + +
71H PHE* 1.3 77.2 - - - +
73H ARG* 1.3 62.2 - - - +
74H VAL* 3.8 11.7 + - + -
96H VAL* 5.6 0.2 - - + -
108H TYR 3.5 1.6 - - - +
109H LEU* 3.4 5.2 - - - +
110H LEU* 2.7 55.3 + - + +
112H ALA* 4.3 17.3 - - + -
120H PHE* 3.9 20.4 - - + -
123H PHE* 4.0 24.0 - - + -
128H LEU* 3.8 24.2 - - + -
137H ALA* 4.2 7.2 - - + -
138H GLN 3.8 1.3 - - - +
139H SER* 3.4 21.3 - - - +
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Residues in contact with ARG 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G ARG* 3.0 52.1 - - - +
102G LEU* 5.6 3.8 - - - +
106G THR* 4.6 5.7 + - - -
109G LEU* 4.3 16.8 - - - +
71H PHE* 4.8 5.1 - - + +
72H ILE* 1.3 74.2 - - - +
74H VAL* 1.3 60.7 + - - +
75H SER* 4.1 0.9 + - - -
102H LEU* 4.7 4.8 - - - +
106H THR* 3.3 30.0 + - + +
108H TYR 3.6 5.4 - - - -
109H LEU* 3.3 29.2 - - + +
137H ALA* 3.2 3.8 - - - -
138H GLN* 2.8 62.6 + - + +
139H SER* 5.7 0.4 - - - -
140H SER* 5.8 2.6 + - - -
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Residues in contact with VAL 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H ILE* 4.0 16.2 - - + -
73H ARG* 1.3 76.3 - - - +
75H SER* 1.3 73.2 + - - +
76H ILE* 4.3 3.4 - - + +
86H PHE* 3.8 26.0 - - + -
106H THR* 4.0 0.8 - - - +
107H ASP* 3.3 10.8 + - - +
108H TYR* 2.8 39.8 + - + +
110H LEU* 3.6 23.8 - - + -
128H LEU* 4.1 13.5 - - + -
134H VAL* 4.2 12.8 - - + -
136H ASP 3.5 6.1 - - - +
137H ALA* 4.2 4.7 - - + -
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Residues in contact with SER 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H ARG 4.1 1.3 + - - -
74H VAL* 1.3 72.1 - - - +
76H ILE* 1.3 55.5 + - - +
105H GLU 5.3 4.0 + - - -
106H THR* 6.0 0.7 - - - -
107H ASP* 3.4 11.5 + - - -
134H VAL* 3.8 2.1 - - - -
135H GLN* 2.8 49.2 + - - +
136H ASP* 2.9 30.6 + - - +
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Residues in contact with ILE 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H VAL* 3.9 4.0 + - + +
75H SER* 1.3 75.6 - - - +
77H ARG* 1.3 75.8 + - - +
78H LYS* 3.7 6.7 + - + +
82H ALA* 3.7 13.2 - - + +
83H ARG* 4.0 34.5 - - + +
86H PHE* 3.6 39.9 - - + -
107H ASP* 2.9 23.4 + - + +
108H TYR* 3.9 17.0 - - + -
133H GLY 3.0 21.3 - - - +
134H VAL* 4.9 1.3 - - - -
135H GLN* 3.4 13.8 - - - +
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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