Contacts of the helix formed by residues 68 - 79 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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836C VAL* 3.7 31.9 - - - +
838C PRO 4.0 10.7 + - - -
840C GLU 3.3 19.5 + - - -
841C ALA 3.4 8.7 + - - -
843C PRO* 5.4 1.9 - - - +
66D CYS 3.6 1.2 + - - -
67D ARG* 1.3 74.7 - - - +
69D ILE* 1.3 66.9 + - - +
70D VAL* 3.3 14.4 + - - +
71D ARG* 2.8 22.9 + - - +
72D THR* 3.0 10.8 + - - -
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Residues in contact with ILE 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841C ALA* 2.8 38.3 + - + +
842C GLU* 3.2 32.1 - - - +
843C PRO* 5.4 1.6 - - + -
871C TYR* 4.5 6.7 - - - +
910C MET* 3.9 19.5 - - + -
62D ILE* 6.0 1.8 - - + -
67D ARG 3.9 1.1 + - - +
68D SER* 1.3 70.9 - - - +
70D VAL* 1.3 52.8 + - - +
72D THR* 3.1 8.7 + - - -
73D LEU* 2.7 59.7 + - + +
89D GLY* 4.0 19.1 - - - +
90D LEU* 5.0 3.1 - - + +
92D GLN* 5.6 1.8 - - + +
93D SER* 3.8 22.2 - - - +
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Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722C ARG* 5.9 1.1 - - - +
814C LEU* 4.8 8.1 - - + -
816C LEU* 3.8 34.5 - - + -
834C ALA* 5.1 0.4 - - + -
836C VAL* 3.9 22.9 - - + -
843C PRO* 3.9 20.0 - - + -
869C ALA* 4.9 1.8 - - + -
871C TYR* 3.8 26.2 - - + +
68D SER* 3.1 6.2 - - - +
69D ILE* 1.3 77.2 - - - +
71D ARG* 1.3 58.1 + - - +
73D LEU* 3.8 7.7 - - + +
74D HIS* 3.0 32.9 + - + +
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Residues in contact with ARG 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788C VAL* 5.2 1.6 - - - +
789C HIS* 3.0 50.5 + - - +
812C TYR* 6.0 3.0 - - - -
814C LEU* 3.7 27.1 - - - +
836C VAL* 3.9 18.0 - - - +
838C PRO* 4.2 12.9 + - - +
64D PRO* 3.6 24.9 - - + -
65D PRO* 3.8 28.0 + - - +
68D SER* 2.8 21.9 + - - +
70D VAL* 1.3 74.1 - - - +
72D THR* 1.3 55.1 + - - +
74D HIS* 4.2 3.6 - - - +
75D GLN* 3.1 34.0 + - + +
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Residues in contact with THR 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ILE* 3.4 24.7 - - + +
63D LEU* 3.3 32.0 - - + +
64D PRO* 3.3 20.5 - - - +
67D ARG* 3.9 1.7 - - - +
68D SER 3.0 11.0 + - - -
69D ILE* 3.5 10.8 - - - -
71D ARG* 1.3 74.8 - - - +
73D LEU* 1.3 61.2 + - + +
75D GLN* 3.2 4.9 + - - +
76D HIS* 3.0 27.2 + - - +
86D VAL* 4.0 20.2 - - + +
89D GLY* 4.8 2.7 - - - -
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Residues in contact with LEU 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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871C TYR* 4.6 10.8 - - + -
910C MET* 4.6 1.3 - - - -
912C LEU* 3.6 37.0 - - + -
926C LEU* 3.5 26.7 - - + -
69D ILE* 2.7 38.8 + - + +
70D VAL* 3.8 4.3 - - + +
72D THR* 1.3 70.8 - - + +
74D HIS* 1.3 67.3 + - - +
76D HIS* 3.3 10.3 + - + +
77D LYS* 3.0 20.1 + - - +
86D VAL* 4.4 17.7 - - + -
90D LEU* 4.5 6.5 - - + -
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Residues in contact with HIS 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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360C VAL* 4.1 13.2 - - + +
720C SER* 5.5 3.8 - - - -
722C ARG* 3.2 61.7 + - + +
789C HIS* 5.4 1.9 + - + -
814C LEU* 6.4 0.7 - - + -
70D VAL* 3.0 19.0 + - + +
71D ARG* 4.2 3.8 - - - +
73D LEU* 1.3 77.2 - - - +
75D GLN* 1.3 64.5 + - + +
77D LYS* 2.8 31.7 + - + +
78D LEU* 3.0 47.0 + - + +
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Residues in contact with GLN 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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382C PHE* 5.2 1.0 - - - -
63D LEU* 4.4 12.1 - - + +
64D PRO* 3.8 22.9 - - + +
71D ARG* 3.1 27.3 + - + +
72D THR* 3.2 8.7 + - - +
74D HIS* 1.3 77.0 + - - +
76D HIS* 1.3 61.9 - - - +
78D LEU* 3.1 20.6 + - - +
80D ARG* 2.9 69.5 + - - +
81D ALA* 3.6 12.8 - - + -
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Residues in contact with HIS 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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970C ASN* 4.3 3.4 - - + +
972C PHE* 6.5 0.4 - + - -
1003C PHE* 3.2 48.1 - + - -
1033C VAL* 5.0 0.3 - - - +
72D THR 3.0 9.1 + - - +
73D LEU* 3.4 13.7 - - + +
75D GLN* 1.3 75.2 - - - +
77D LYS* 1.3 61.4 + - - +
79D GLY* 3.4 13.0 + - - -
81D ALA* 3.4 23.5 + - - +
83D TRP* 3.4 33.2 - + + -
86D VAL* 3.4 39.2 - - + +
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Residues in contact with LYS 77 (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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358C PRO* 4.6 1.4 - - - +
360C VAL* 3.1 42.5 + - + +
723C LYS* 4.2 20.6 - - - +
913C TYR* 5.7 7.0 - - - -
955C SER 5.6 4.5 - - - -
1003C PHE* 4.5 5.4 - - + -
1005C ASN* 3.1 53.7 + - - +
1006C VAL* 4.6 5.0 - - - +
1033C VAL* 3.4 17.2 - - - +
73D LEU 3.0 11.8 + - - +
74D HIS* 2.8 26.6 + - + +
76D HIS* 1.3 77.6 - - - +
78D LEU* 1.3 58.9 + - + +
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Residues in contact with LEU 78 (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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327C ARG* 5.8 1.0 + - - +
328C LEU* 3.9 12.5 - - + +
358C PRO* 3.4 25.0 - - + +
360C VAL* 3.7 30.3 - - + -
381C ALA* 3.9 21.8 - - + -
382C PHE* 4.7 18.4 - - + -
720C SER* 5.7 2.5 - - - -
1033C VAL* 3.9 4.4 - - - +
74D HIS* 3.0 39.9 + - + +
75D GLN* 3.1 23.0 + - - +
77D LYS* 1.3 75.7 - - - +
79D GLY* 1.3 56.2 + - - +
80D ARG* 3.2 21.6 + - + +
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Residues in contact with GLY 79 (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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327C ARG* 3.5 26.7 + - - -
328C LEU* 5.9 0.4 - - - -
1033C VAL* 3.7 17.0 - - - -
75D GLN 3.3 2.0 + - - -
76D HIS 3.4 6.4 + - - -
77D LYS 3.3 4.6 + - - -
78D LEU* 1.3 78.6 - - - +
80D ARG* 1.3 56.5 + - - +
81D ALA 3.2 12.3 + - - +
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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