Contacts of the helix formed by residues 84 - 98 (chain P) in PDB entry 3E8E
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 GLN 84 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54P PHE* 4.0 28.7 - - + -
79P VAL* 2.8 25.1 + - + +
82P LEU* 3.5 14.8 + - + +
83P LYS* 1.3 79.7 + - - +
85P ILE* 1.3 64.6 + - - +
86P GLU 3.5 2.0 - - - -
87P HIS* 2.7 35.3 + - + +
88P THR* 3.0 27.8 + - + +
187P PHE* 3.5 12.9 - - - -
23Q HIS* 4.8 1.8 - - + -
24Q ASP* 3.0 48.2 + - - +
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Residues in contact with ILE 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79P VAL* 3.6 6.3 - - - +
80P VAL* 3.6 45.5 - - + +
83P LYS* 3.6 3.6 - - - -
84P GLN* 1.3 76.9 - - - +
86P GLU* 1.3 65.7 + - - +
88P THR* 2.9 20.3 + - - -
89P LEU* 3.1 19.7 + - + +
346P GLU* 3.6 42.0 - - + +
347P PHE* 4.0 9.9 - - + -
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Residues in contact with GLU 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84P GLN 3.5 0.2 - - - -
85P ILE* 1.3 83.2 - - + +
87P HIS* 1.3 61.3 + - + +
89P LEU* 3.2 11.1 + - + +
90P ASN* 2.8 45.3 + - - +
189P LYS* 3.9 26.2 + - - -
197P TPO 4.1 8.4 + - - -
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Residues in contact with HIS 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83P LYS 5.2 2.9 - - - -
84P GLN* 2.7 36.2 + - + +
85P ILE 3.2 0.8 - - - -
86P GLU* 1.3 82.9 - - + +
88P THR* 1.3 56.5 + - + +
90P ASN* 3.2 18.2 + - - +
91P GLU* 2.9 26.2 + - - +
165P ARG* 3.8 9.5 + - - -
186P GLY* 3.2 26.8 - - - +
187P PHE* 3.7 14.4 - + - -
197P TPO 2.7 42.1 + - + +
199P CYS* 4.7 0.4 - - - -
24Q ASP* 3.6 20.9 - - - -
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Residues in contact with THR 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P PHE* 4.7 3.6 - - + -
74P LEU* 3.6 26.5 - - + -
79P VAL* 3.4 20.4 - - + -
84P GLN* 3.0 20.4 + - + +
85P ILE 2.9 14.2 + - - -
87P HIS* 1.3 74.7 - - + +
89P LEU* 1.3 63.9 + - - +
91P GLU* 3.5 11.8 - - - +
92P LYS* 3.2 22.5 + - - +
116P LEU* 3.8 13.7 - - + +
118P MET* 4.8 1.7 - - - +
347P PHE* 3.7 15.9 - - - -
350P PHE* 4.0 6.2 - - - -
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Residues in contact with LEU 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85P ILE* 3.1 31.2 + - + +
86P GLU* 3.5 11.0 - - + +
88P THR* 1.3 81.8 + - - +
90P ASN* 1.3 64.5 + - - +
92P LYS* 3.5 4.5 + - - +
93P ARG* 3.0 27.5 + - - +
346P GLU 4.3 7.2 - - - +
347P PHE* 4.6 9.9 - - + -
349P GLU* 3.7 47.4 - - + +
350P PHE* 3.9 33.7 - - + +
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Residues in contact with ASN 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P TRP* 5.8 4.2 - - - -
86P GLU* 2.8 37.3 + - - +
87P HIS* 3.3 26.9 - - - +
89P LEU* 1.3 73.1 - - - +
91P GLU* 1.3 56.8 + - - +
93P ARG* 3.2 3.7 + - - +
94P ILE* 2.8 45.8 + - + +
188P ALA 3.2 23.8 + - - +
189P LYS* 4.1 21.7 - - - +
190P ARG 5.3 1.4 + - - -
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Residues in contact with GLU 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P PHE* 6.0 0.5 - - - -
72P LYS* 3.1 24.8 + - - -
74P LEU* 4.6 4.0 - - - +
87P HIS 2.9 14.9 + - - +
88P THR* 3.5 16.6 - - - +
89P LEU 3.3 0.2 - - - -
90P ASN* 1.3 72.9 - - - +
92P LYS* 1.3 63.3 + - - +
94P ILE* 4.2 1.8 - - - +
95P LEU* 3.0 36.5 + - + +
118P MET* 3.6 23.9 - - - +
185P PHE* 3.6 20.8 + - - +
186P GLY* 3.5 21.7 + - - -
351P G98 2.5 32.4 + - - +
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Residues in contact with LYS 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P PRO* 4.7 11.9 - - - +
34P ALA 4.3 4.8 + - - -
35P GLN* 3.6 26.1 - - - +
88P THR 3.2 5.8 + - - +
89P LEU* 4.0 4.0 - - - +
91P GLU* 1.3 78.8 - - - +
93P ARG* 1.3 68.9 + - - +
95P LEU* 3.4 4.5 + - - +
96P GLN* 3.1 30.3 + - + +
106P LEU* 4.0 8.1 - - + +
109P SER* 3.8 24.0 + - - +
118P MET* 4.2 9.6 - - - -
349P GLU 4.2 4.6 + - - -
350P PHE* 2.9 74.2 + - + +
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Residues in contact with ARG 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L TRP* 6.1 1.0 - - - +
190L ARG* 6.1 0.8 - - - +
30P TRP* 3.4 70.4 + - + +
31P GLU* 5.6 0.4 - - - +
33P PRO* 4.9 11.0 - - + +
89P LEU 3.0 18.9 + - - +
90P ASN* 3.9 2.9 - - - +
92P LYS* 1.3 81.8 - - - +
94P ILE* 1.3 66.4 + - - +
96P GLN* 2.7 40.3 + - - +
97P ALA* 3.5 4.9 + - - +
349P GLU* 4.8 16.6 + - - +
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Residues in contact with ILE 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P PHE* 5.1 0.2 - - - -
30P TRP* 3.9 18.8 - - + -
90P ASN* 2.8 26.7 + - + +
91P GLU* 4.2 2.2 - - - +
93P ARG* 1.3 70.6 - - - +
95P LEU* 1.3 63.5 + - - +
97P ALA* 3.1 11.8 + - - +
98P VAL* 3.1 31.4 + - + +
162P LEU* 3.8 33.2 - - + -
185P PHE* 4.0 21.3 - - + -
188P ALA* 3.5 41.7 - - + +
189P LYS* 3.6 9.4 - - - +
190P ARG 4.2 0.9 - - - +
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Residues in contact with LEU 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91P GLU* 3.0 31.4 + - + +
92P LYS 3.8 3.4 - - - +
93P ARG 3.3 0.2 - - - -
94P ILE* 1.3 78.5 - - - +
96P GLN* 1.3 60.2 + - - +
97P ALA 3.4 0.5 + - - -
98P VAL* 3.5 24.1 + - + +
103P LEU* 6.1 0.2 - - + -
104P VAL 3.8 21.5 - - - +
105P LYS* 6.0 0.2 - - - -
106P LEU* 4.0 29.4 + - + +
118P MET* 4.5 4.7 - - - -
185P PHE* 3.9 33.0 - - + -
351P G98 3.5 44.0 - - + +
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Residues in contact with GLN 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P LYS* 3.1 37.9 + - - +
30P TRP* 4.2 3.0 - - - +
32P ASN 4.3 1.0 - - - +
33P PRO* 3.5 35.8 - - + +
34P ALA* 4.5 11.4 + - + +
92P LYS* 3.1 20.6 + - + +
93P ARG* 2.7 33.6 + - - +
95P LEU* 1.3 75.2 - - - +
97P ALA* 1.3 64.2 + - - +
98P VAL 4.7 1.8 - - - +
106P LEU* 4.2 14.5 - - + +
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Residues in contact with ALA 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P ASP 4.8 0.2 - - - -
26P PHE* 3.5 54.6 - - + +
29P LYS* 3.6 21.8 + - - +
30P TRP* 3.9 9.4 - - + +
93P ARG 3.7 13.5 - - - +
94P ILE 3.1 2.5 + - - +
96P GLN* 1.3 89.1 - - - +
98P VAL* 1.3 61.8 + - - +
99P ASN* 5.2 0.2 - - - +
156P TYR* 4.7 0.7 + - - -
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Residues in contact with VAL 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P PHE* 4.2 6.5 - - + -
29P LYS* 4.3 4.2 + - - -
94P ILE* 3.2 31.0 - - + +
95P LEU* 3.5 31.8 - - + +
96P GLN 4.7 1.7 - - - +
97P ALA* 1.3 80.6 - - - +
99P ASN* 1.3 65.2 + - - +
103P LEU* 4.0 19.3 - - + -
104P VAL 5.7 1.3 - - - +
105P LYS* 5.9 2.6 - - - +
156P TYR* 3.5 18.6 - - + +
157P LEU* 4.5 5.4 - - + -
162P LEU* 3.9 17.9 - - + -
185P PHE* 5.1 2.2 - - + -
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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