Contacts of the strand formed by residues 65 - 73 (chain A) in PDB entry 2MF9
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 VAL 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A GLY 3.4 6.2 + - - +
64A GLN* 1.3 73.1 - - - +
66A VAL* 1.3 60.1 + - - +
67A THR* 5.5 0.3 - - - +
87A VAL* 3.5 21.1 - - + +
88A PHE* 2.9 17.3 - - - +
89A THR* 3.9 20.2 - - + +
146A THR 5.1 0.2 - - - -
147A ALA 4.0 0.2 - - - -
148A VAL* 2.9 47.5 + - + +
150A LEU* 4.2 31.3 - - + +
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Residues in contact with VAL 66 (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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60A PRO* 3.5 20.9 - - + -
64A GLN* 3.8 11.9 - - + +
65A VAL* 1.3 76.7 - - - +
67A THR* 1.3 58.7 + - - +
68A VAL* 3.6 0.6 + - + -
86A LEU 2.8 14.9 - - - +
87A VAL* 2.9 11.3 - - - -
88A PHE* 3.1 38.6 + - + +
90A LEU* 4.9 2.5 - - + -
103A VAL* 3.9 15.0 - - + -
144A LEU* 3.6 9.0 - - + -
146A THR 3.3 8.7 - - - +
147A ALA* 3.4 29.8 - - + -
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Residues in contact with THR 67 (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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65A VAL 5.5 0.2 - - - +
66A VAL* 1.3 70.3 - - - +
68A VAL* 1.3 61.2 + - - +
85A GLU* 3.7 28.0 - - + +
86A LEU 3.3 5.4 - - - -
87A VAL* 3.3 28.7 - - + -
143A THR 3.4 0.3 - - - +
144A LEU* 3.6 3.3 - - - -
145A LYS* 3.0 28.5 + - - +
146A THR* 2.8 50.0 + - + +
148A VAL* 6.3 0.9 - - + -
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Residues in contact with VAL 68 (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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66A VAL* 4.5 0.7 - - + -
67A THR* 1.3 78.1 - - - +
69A HIS* 1.3 61.0 + - - +
70A LEU* 3.9 3.6 + - + +
83A GLU 4.0 0.3 - - - +
84A PRO 4.5 0.4 - - - -
85A GLU* 3.3 3.4 - - - -
86A LEU* 2.7 59.6 + - + +
88A PHE* 3.7 28.0 - - + -
99A LEU* 3.7 19.5 - - + -
103A VAL* 4.0 17.7 - - + -
106A MET* 4.8 0.7 - - + -
142A VAL* 4.5 14.8 - - + -
143A THR 3.1 7.0 - - - +
144A LEU* 4.1 15.9 - - + -
145A LYS* 4.7 0.4 - - - -
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Residues in contact with HIS 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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68A VAL* 1.3 72.8 - - - +
70A LEU* 1.3 66.2 + - - +
71A GLN* 3.1 34.5 + - - +
82A GLU* 3.8 17.2 + - + +
83A GLU 3.0 18.4 + - - -
84A PRO* 3.2 34.5 + - + +
141A GLU 2.9 7.1 - - - +
142A VAL* 3.0 2.1 - - - -
143A THR* 2.7 56.1 + - - +
145A LYS* 4.2 6.3 - - + +
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Residues in contact with LEU 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 VAL* 3.9 4.1 - - + -
69A HIS* 1.3 74.3 - - - +
71A GLN* 1.3 61.6 + - - +
72A THR* 3.3 21.1 - - - +
81A GLN* 3.6 20.2 - - + +
82A GLU* 3.4 1.8 - - - -
83A GLU* 2.7 75.4 + - + +
86A LEU* 4.9 7.9 - - + -
96A ILE* 5.4 5.2 - - + -
99A LEU* 5.4 7.2 - - + -
122A TYR* 4.4 7.9 - - + +
128A ARG* 4.9 3.8 - - - +
140A LEU* 4.7 10.3 - - + -
141A GLU 3.1 3.6 - - - +
142A VAL* 3.5 22.7 - - + -
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Residues in contact with GLN 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 HIS* 3.1 38.9 + - - +
70A LEU* 1.3 72.5 - - - +
72A THR* 1.3 60.8 + - - +
79A ARG* 3.4 36.5 + - - +
81A GLN 3.1 9.4 - - - +
82A GLU* 3.7 20.3 - - + +
140A LEU* 3.7 0.5 - - - -
141A GLU* 2.8 77.1 + - - +
143A THR* 4.8 3.5 + - - -
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Residues in contact with THR 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 LEU* 3.3 22.0 - - - +
71A GLN* 1.3 73.7 - - - +
73A SER* 1.3 61.5 + - - +
79A ARG* 3.0 5.0 - - - -
80A VAL* 2.7 33.5 + - + +
81A GLN* 2.8 27.0 + - - +
122A TYR* 5.7 0.2 - - - -
138A LEU* 3.2 42.3 - - + +
139A CYS 3.5 3.4 - - - +
140A LEU* 3.1 26.4 - - + +
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Residues in contact with SER 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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72A THR* 1.3 79.9 - - - +
74A LEU* 1.3 70.8 + - - +
77A GLY* 3.8 14.4 + - - -
78A THR 3.2 6.3 - - - -
79A ARG* 2.7 39.5 + - - +
113A MET* 5.6 1.7 - - - +
138A LEU* 3.7 2.3 - - - +
139A CYS* 2.6 45.8 + - - -
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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