Contacts of the helix formed by residues 82 - 101 (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 82 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E GLU* 3.2 25.9 + - - +
63F LEU* 5.0 0.4 - - - +
80F ARG 4.2 1.4 + - - -
81F ALA* 1.3 71.9 - - - +
83F TRP* 1.3 64.7 + - - +
84F PRO* 3.4 14.8 - - - +
85F SER* 2.9 38.4 + - - -
86F VAL* 3.1 5.4 + - - +
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Residues in contact with TRP 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926E LEU* 5.9 2.7 - - + -
953E TRP* 3.3 46.6 - + + -
970E ASN* 3.0 36.9 - - + +
1079E GLU* 5.3 9.0 - - + -
76F HIS* 3.4 32.7 - + + -
81F ALA 3.3 3.4 + - - -
82F SER* 1.3 69.7 - - - +
84F PRO* 1.3 72.7 - - + +
85F SER 2.7 1.0 + - - -
86F VAL* 2.9 26.4 + - + -
87F GLN* 2.7 68.6 + - + +
90F LEU* 3.8 13.9 - - + -
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Residues in contact with PRO 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E PRO* 5.3 5.6 - - + +
116E SER 4.8 3.8 - - - +
117E GLU* 3.8 39.5 - - + +
1079E GLU* 5.4 7.4 - - - +
60F PRO* 4.9 6.8 - - - +
82F SER* 3.4 12.3 - - - +
83F TRP* 1.3 100.4 - - + +
85F SER* 1.3 59.2 + - - +
87F GLN* 3.3 12.4 - - + +
88F GLN* 3.3 19.4 + - - +
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Residues in contact with SER 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E GLU* 5.9 1.2 - - - +
60F PRO 5.2 1.3 - - - -
61F GLN 4.4 11.2 + - - -
62F ILE* 3.5 6.0 - - - +
63F LEU* 3.2 36.3 + - - +
82F SER* 2.9 27.4 + - - -
83F TRP 2.7 4.6 + - - -
84F PRO* 1.3 73.0 - - - +
86F VAL* 1.3 57.6 + - - -
88F GLN* 2.8 27.3 + - - +
89F GLY 3.0 9.0 + - - -
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Residues in contact with VAL 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F LEU* 3.5 8.9 - - + +
72F THR* 4.0 15.4 - - + +
73F LEU* 4.4 19.1 - - + -
76F HIS* 3.4 52.0 - - + +
81F ALA 4.0 2.5 - - - +
82F SER 3.2 15.9 - - - +
83F TRP* 3.4 20.9 - - + +
85F SER* 1.3 71.5 - - - +
87F GLN* 1.3 64.2 + - - +
89F GLY* 3.0 3.5 + - - -
90F LEU* 2.9 28.8 + - + +
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Residues in contact with GLN 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953E TRP* 3.3 28.8 - - - -
1080E ARG* 4.8 2.4 + - - -
83F TRP* 2.7 54.0 + - - +
84F PRO* 3.3 19.1 - - + +
86F VAL* 1.3 71.9 - - - +
88F GLN* 1.3 59.7 - - - +
90F LEU* 3.1 8.9 + - - +
91F GLN* 2.8 30.9 + - - +
347F ARG 4.1 10.7 - - - +
348F TYR* 4.4 10.0 - - + -
349F ASN* 5.6 2.1 + - + +
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Residues in contact with GLN 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F PRO* 3.2 51.3 - - + +
62F ILE* 3.8 17.0 - - + +
84F PRO 3.3 6.0 + - - +
85F SER 2.8 14.1 + - - +
87F GLN* 1.3 76.5 - - - +
89F GLY* 1.3 57.5 + - - +
91F GLN* 3.2 38.3 + - - +
92F GLN* 2.9 39.7 + - - +
95F LEU* 5.9 1.6 - - - +
349F ASN* 5.8 1.4 - - - +
376F ASP* 5.1 6.6 + - - +
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Residues in contact with GLY 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F ILE* 3.3 29.7 - - - +
69F ILE* 4.1 12.8 - - - +
72F THR* 4.8 4.5 - - - -
85F SER 3.0 6.5 + - - -
86F VAL 3.0 7.8 + - - -
88F GLN* 1.3 74.2 - - - +
90F LEU* 1.3 58.9 + - - +
92F GLN* 3.2 7.7 + - - +
93F SER* 2.8 27.7 + - - -
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Residues in contact with LEU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910E MET* 4.2 8.3 - - + -
926E LEU* 3.6 29.8 - - + -
927E MET* 3.9 21.6 - - + +
953E TRP* 3.8 28.0 - - + +
69F ILE* 5.1 2.9 - - + -
73F LEU* 4.5 7.0 - - + -
83F TRP* 3.8 25.4 - - + -
86F VAL* 2.9 19.3 + - + +
87F GLN* 3.4 7.2 - - - +
89F GLY* 1.3 73.6 - - - +
91F GLN* 1.3 52.6 + - - +
93F SER* 2.8 7.5 + - - -
94F PHE* 2.7 35.7 + - - +
348F TYR* 3.7 17.3 - - + +
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Residues in contact with GLN 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F GLN* 2.8 20.1 + - + +
88F GLN* 3.2 38.8 + - - +
90F LEU* 1.3 71.9 - - - +
92F GLN* 1.3 58.1 + - - +
94F PHE* 3.5 2.5 - - - +
95F LEU* 2.8 33.1 + - + +
348F TYR* 3.4 23.8 - - + +
349F ASN* 2.6 51.8 + - - +
350F LEU* 3.8 23.0 - - + +
376F ASP* 4.3 14.3 + - - -
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Residues in contact with GLN 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841E ALA* 4.5 18.8 - - + +
62F ILE* 3.4 33.4 - - - +
67F ARG* 5.0 3.0 + - - +
69F ILE* 5.6 1.9 - - + +
88F GLN* 2.9 25.1 + - - +
89F GLY 3.4 8.3 + - - +
91F GLN* 1.3 73.8 - - - +
93F SER* 1.3 68.0 + - - +
95F LEU* 3.1 14.2 + - + +
96F HIS* 2.9 23.4 + - - +
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Residues in contact with SER 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842E GLU* 3.0 30.5 + - - +
910E MET* 3.2 19.3 - - - +
927E MET* 3.8 7.9 - - - +
69F ILE* 3.8 18.6 - - - +
89F GLY 2.8 13.0 + - - -
90F LEU* 2.8 12.0 + - - -
92F GLN* 1.3 76.3 - - - +
94F PHE* 1.3 60.8 + - - +
96F HIS* 3.3 5.8 + - - +
97F THR* 3.2 25.3 + - - +
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Residues in contact with PHE 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909E ILE* 6.1 3.8 - - + -
927E MET* 3.6 11.5 - - + +
90F LEU 2.7 15.0 + - - +
91F GLN 3.5 6.3 - - - +
93F SER* 1.3 67.9 - - - +
95F LEU* 1.3 70.9 + - - +
96F HIS 2.9 1.6 - - - -
97F THR* 2.5 30.8 + - - -
98F LEU* 2.9 29.1 + - + +
101F TYR* 3.9 16.8 - + - -
345F HIS* 3.6 21.1 - + - -
348F TYR* 3.7 29.6 - + + -
350F LEU* 3.7 32.3 - - + -
374F VAL* 5.9 0.2 - - + -
400F PHE* 4.1 17.0 - + - -
404F GLY 3.2 22.2 - - - -
405F ASP* 4.9 0.4 - - - -
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Residues in contact with LEU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F GLN* 5.9 0.9 - - - +
91F GLN* 2.8 29.1 + - + +
92F GLN* 3.1 14.6 + - + +
94F PHE* 1.3 75.2 - - - +
96F HIS* 1.3 60.2 + - - +
98F LEU* 3.3 35.3 + - + +
99F ASP* 3.5 13.4 + - - +
350F LEU* 4.1 25.1 - - + -
374F VAL* 4.3 2.2 - - + -
383F MET* 3.7 58.1 - - + +
384F CYS* 4.6 2.8 - - - +
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Residues in contact with HIS 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842E GLU* 4.1 26.8 + - + +
844E LYS* 3.4 34.7 + - - -
92F GLN 2.9 11.1 + - - +
93F SER 3.5 9.4 + - - +
94F PHE 2.8 1.4 + - - -
95F LEU* 1.3 73.1 - - - +
97F THR* 1.3 67.4 + - - +
98F LEU 3.0 1.8 - - - -
99F ASP* 3.1 32.9 + - + +
100F SER* 3.9 2.9 + - - -
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Residues in contact with THR 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842E GLU* 6.1 1.3 - - - +
909E ILE* 4.5 18.2 - - + +
927E MET* 5.3 0.2 - - - +
93F SER* 3.4 16.2 - - - +
94F PHE* 2.5 32.5 + - - -
96F HIS* 1.3 78.2 - - + +
98F LEU* 1.3 56.7 + - - +
100F SER* 3.0 19.7 + - - -
101F TYR* 3.0 28.2 + - - -
420F GLN* 3.7 32.4 - - - +
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Residues in contact with LEU 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F PHE* 2.9 31.8 + - + +
95F LEU* 3.3 26.5 - - + +
96F HIS 3.0 0.4 - - - -
97F THR* 1.3 76.5 + - - +
99F ASP* 1.3 61.8 + - - +
100F SER 3.3 0.2 - - - -
101F TYR* 3.2 49.3 + - + +
374F VAL* 3.9 22.2 - - + -
384F CYS* 3.5 25.9 - - - -
386F LEU* 3.7 26.4 - - + +
400F PHE* 4.3 9.9 - - + -
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Residues in contact with ASP 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F LEU 3.5 15.0 + - - +
96F HIS* 3.1 24.2 + - + +
98F LEU* 1.3 79.5 - - - +
100F SER* 1.3 55.6 + - - +
102F ARG* 3.4 28.4 + - - +
384F CYS* 3.7 24.1 - - - +
385F GLN 5.1 2.4 - - - +
386F LEU* 5.4 1.9 - - - +
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Residues in contact with SER 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F HIS 3.9 2.1 + - - -
97F THR* 3.0 20.0 + - - -
99F ASP* 1.3 77.5 - - - +
101F TYR* 1.4 54.8 + - - +
102F ARG* 2.8 23.7 + - - +
103F ILE* 3.8 7.6 + - - +
420F GLN* 3.1 24.0 + - - +
421F GLU* 3.9 18.2 + - - +
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Residues in contact with TYR 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909E ILE* 5.1 4.1 - - + +
94F PHE* 3.9 13.9 - + - -
97F THR* 3.0 38.5 + - - -
98F LEU* 3.2 40.4 - - + +
100F SER* 1.4 72.5 - - - +
102F ARG* 1.3 51.1 + - - +
103F ILE 2.3 35.2 + - - +
386F LEU* 4.6 6.3 - - + -
400F PHE* 4.5 9.4 - + - -
405F ASP* 2.8 50.2 + - - +
406F THR* 4.1 2.5 - - - -
407F LEU* 4.9 1.3 - - + -
418F TRP* 3.7 33.8 - - + -
419F SER* 3.2 11.2 + - - +
420F GLN* 3.8 25.4 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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