Contacts of the helix formed by residues 68 - 79 (chain F) in PDB entry 3EI4
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 SER 68 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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836E VAL* 3.7 31.1 - - - +
838E PRO 4.0 10.3 + - - -
840E GLU 3.2 19.2 + - - -
841E ALA 3.3 9.0 + - - -
842E GLU 5.7 0.2 - - - -
843E PRO* 5.3 2.3 - - - +
66F CYS 3.6 1.6 + - - -
67F ARG* 1.3 74.1 - - - +
69F ILE* 1.3 66.5 + - - +
70F VAL* 3.3 14.7 + - - +
71F ARG* 2.7 23.6 + - - +
72F THR* 3.0 10.7 + - - -
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Residues in contact with ILE 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841E ALA* 2.7 39.2 + - + +
842E GLU* 3.1 33.0 - - - +
843E PRO* 5.4 2.0 - - + -
871E TYR* 4.5 6.7 - - - +
910E MET* 3.8 18.8 - - + -
62F ILE* 6.0 2.2 - - + -
67F ARG 3.9 0.8 + - - +
68F SER* 1.3 70.1 - - - +
70F VAL* 1.3 52.2 + - + +
72F THR* 3.0 8.5 + - - +
73F LEU* 2.7 58.5 + - + +
89F GLY* 4.1 17.7 - - - +
90F LEU* 5.1 3.4 - - + -
92F GLN* 5.6 1.6 - - + +
93F SER* 3.8 22.7 - - - +
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Residues in contact with VAL 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722E ARG* 6.0 1.1 - - - +
814E LEU* 4.9 7.4 - - + -
816E LEU* 3.8 35.7 - - + -
834E ALA* 5.1 0.4 - - + -
836E VAL* 3.9 18.6 - - + -
843E PRO* 3.8 20.9 - - + -
869E ALA* 4.9 1.6 - - + -
871E TYR* 3.6 26.0 - - + +
68F SER* 2.9 8.5 + - - +
69F ILE* 1.3 76.7 - - - +
71F ARG* 1.3 58.5 + - - +
73F LEU* 3.7 8.6 - - + +
74F HIS* 2.9 33.8 + - + +
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Residues in contact with ARG 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788E VAL* 5.3 1.6 - - - +
789E HIS* 3.0 49.5 + - - +
812E TYR* 5.9 3.6 - - - -
814E LEU* 3.7 27.5 - - - +
836E VAL* 3.8 17.6 - - - +
838E PRO* 4.1 13.5 + - - +
64F PRO* 3.5 24.9 - - + -
65F PRO* 3.9 27.2 + - - +
68F SER* 2.7 20.7 + - - +
70F VAL* 1.3 75.0 - - - +
72F THR* 1.3 59.8 + - - +
74F HIS* 4.2 3.9 - - - +
75F GLN* 3.1 31.7 + - + +
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Residues in contact with THR 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F ILE* 3.4 23.5 - - + +
63F LEU* 3.3 32.0 - - + +
64F PRO* 3.4 20.0 - - - +
67F ARG* 3.9 2.4 - - - +
68F SER 3.0 11.3 + - - -
69F ILE* 3.4 11.6 - - - -
71F ARG* 1.3 75.0 - - - +
73F LEU* 1.3 59.7 + - + +
75F GLN* 3.3 5.1 + - - +
76F HIS* 3.0 26.9 + - - +
86F VAL* 4.0 21.1 - - + +
89F GLY* 4.8 2.9 - - - -
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Residues in contact with LEU 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871E TYR* 4.6 11.2 - - + -
910E MET* 4.6 1.1 - - - -
912E LEU* 3.6 37.9 - - + -
926E LEU* 3.4 26.9 - - + -
69F ILE* 2.7 39.9 + - + +
70F VAL* 3.7 4.5 - - + +
72F THR* 1.3 71.2 - - + +
74F HIS* 1.3 67.4 + - - +
76F HIS* 3.3 10.8 + - + +
77F LYS* 3.0 19.8 + - - +
86F VAL* 4.4 17.9 - - + -
90F LEU* 4.5 6.7 - - + -
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Residues in contact with HIS 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360E VAL* 4.1 13.6 - - + +
720E SER* 5.6 3.1 - - - -
722E ARG* 3.2 61.7 + - + +
789E HIS* 5.4 1.7 - - + -
814E LEU* 6.4 0.4 - - + -
70F VAL* 2.9 19.9 + - + +
71F ARG* 4.2 3.8 - - - +
73F LEU* 1.3 76.8 - - - +
75F GLN* 1.3 66.5 + - - +
77F LYS* 2.8 31.1 + - + +
78F LEU* 3.0 47.2 + - + +
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Residues in contact with GLN 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382E PHE* 5.3 0.3 - - - -
63F LEU* 4.4 12.1 - - + +
64F PRO* 3.8 23.5 - - + +
71F ARG* 3.1 26.8 + - + +
72F THR* 3.3 8.5 - - - +
74F HIS* 1.3 76.7 + - - +
76F HIS* 1.3 62.0 + - - +
78F LEU* 3.1 20.8 + - - +
80F ARG* 2.8 70.7 + - - +
81F ALA* 3.6 12.8 - - + -
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Residues in contact with HIS 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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970E ASN* 4.2 3.6 - - + +
972E PHE* 6.4 0.4 - + - -
1003E PHE* 3.3 45.5 - + - -
1033E VAL* 5.1 0.2 - - - +
72F THR 3.0 9.3 + - - +
73F LEU* 3.5 13.5 - - + +
74F HIS 3.2 0.2 - - - -
75F GLN* 1.3 75.2 - - - +
77F LYS* 1.3 62.7 + - - +
79F GLY* 3.4 13.0 + - - -
81F ALA* 3.4 23.6 + - - +
83F TRP* 3.4 33.6 - + + -
86F VAL* 3.4 38.3 - - + +
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Residues in contact with LYS 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358E PRO* 4.6 1.7 - - - +
360E VAL* 3.2 41.4 + - + +
723E LYS* 4.2 20.4 - - - +
913E TYR* 5.6 7.6 - - - -
955E SER 5.5 5.6 - - - -
1003E PHE* 4.4 6.0 - - + -
1005E ASN* 3.1 52.9 + - - +
1006E VAL* 4.7 5.0 - - - +
1033E VAL* 3.4 16.3 - - - +
73F LEU 3.0 11.8 + - - +
74F HIS* 2.8 27.3 + - + +
76F HIS* 1.3 77.7 - - - +
78F LEU* 1.3 58.9 + - + +
79F GLY 3.4 1.0 + - - -
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Residues in contact with LEU 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327E ARG* 5.8 0.3 + - - -
328E LEU* 4.0 12.7 - - + +
358E PRO* 3.5 23.4 - - + +
360E VAL* 3.8 29.4 - - + -
381E ALA* 3.8 20.9 - - + -
382E PHE* 4.5 17.9 - - + -
720E SER* 5.7 2.0 - - - -
722E ARG* 5.6 0.7 - - - +
1033E VAL* 3.9 4.3 - - - +
74F HIS* 3.0 39.4 + - + +
75F GLN* 3.1 23.3 + - - +
77F LYS* 1.3 75.2 - - - +
79F GLY* 1.3 56.5 - - - +
80F ARG* 3.2 20.6 + - + +
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Residues in contact with GLY 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327E ARG* 3.6 26.8 + - - -
328E LEU* 6.0 0.4 - - - -
1033E VAL* 3.8 16.8 - - - -
76F HIS 3.4 8.4 + - - -
77F LYS 3.2 4.8 + - - -
78F LEU* 1.3 77.6 - - - +
80F ARG* 1.3 57.8 + - - +
81F ALA 3.2 12.8 + - - +
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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