Contacts of the helix formed by residues 93 - 104 (chain C) in PDB entry 5M5X
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 93 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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743B ARG* 4.0 10.3 + - - +
745B GLN* 3.0 35.3 + - - +
800B TYR* 4.1 0.2 - - - -
802B THR* 3.9 24.2 + - - +
804B TYR* 4.5 6.3 + - - -
906B ARG* 3.0 31.2 - - - +
88C ASN* 5.7 2.5 - - - -
90C SER 5.3 1.1 - - - -
91C VAL 3.2 9.9 + - - +
92C ILE* 1.3 79.8 - - - +
94C ASP* 1.3 64.5 + - - +
95C GLU* 3.1 27.1 + - - +
96C VAL* 3.4 15.3 - - + +
97C LEU* 3.2 21.0 + - - +
1J MET* 5.1 0.3 - - - +
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Residues in contact with ASP 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906B ARG* 3.8 13.0 + - - +
85C PHE* 3.0 23.6 - - - +
88C ASN* 2.3 35.5 + - - +
93C GLN* 1.3 76.5 - - - +
95C GLU* 1.3 62.8 + - - +
97C LEU* 3.1 5.2 + - - +
98C ALA* 2.9 29.3 + - - +
60L ARG* 3.3 24.8 + - - -
65L VAL* 4.4 0.5 - - - +
67L PHE* 3.1 37.5 - - + -
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Residues in contact with GLU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B TYR* 3.2 27.3 + - + +
802B THR* 4.2 6.4 - - - +
881B TYR* 5.0 6.5 - - + -
906B ARG* 4.2 17.2 + - - +
908B ARG* 3.9 32.8 + - - +
93C GLN* 3.1 26.6 + - + +
94C ASP* 1.3 79.9 + - - +
96C VAL* 1.3 57.2 + - - +
98C ALA* 3.9 5.4 - - - +
99C HIS* 3.1 26.5 + - - +
67L PHE* 3.9 33.6 - - + -
68L GLU 4.5 1.5 - - - +
70L ARG 4.0 7.1 - - - +
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745B GLN* 3.2 32.1 - - - +
800B TYR* 3.7 20.2 - - + +
92C ILE* 3.9 21.5 - - + -
93C GLN* 3.4 32.0 + - + +
94C ASP 3.1 0.8 - - - -
95C GLU* 1.3 76.5 - - - +
97C LEU* 1.3 60.1 + - - +
99C HIS* 3.1 7.0 + - + +
100C ARG* 2.9 36.9 + - + +
1J MET* 5.2 0.2 - - + -
2J ILE* 5.0 5.4 - - + -
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Residues in contact with LEU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C PHE* 3.6 24.9 - - + -
88C ASN* 5.5 4.5 - - - +
92C ILE* 3.7 26.2 - - + +
93C GLN 3.2 18.7 + - - +
94C ASP* 3.1 6.3 + - - +
96C VAL* 1.3 77.2 - - - +
98C ALA* 1.3 61.0 + - - +
100C ARG* 3.3 4.8 + - + +
101C ILE* 3.0 45.5 + - + +
136C LEU* 5.2 2.5 - - + -
193C LEU* 4.3 17.3 - - + +
194C ALA* 4.4 11.0 - - + -
202C ILE* 5.2 12.8 - - + -
204C LEU* 3.6 18.6 - - + -
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Residues in contact with ALA 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C VAL* 3.8 12.1 - - + -
85C PHE* 3.5 27.4 - - + -
94C ASP 2.9 10.5 + - - +
95C GLU 4.0 2.9 - - - +
97C LEU* 1.3 75.3 - - - +
99C HIS* 1.3 61.7 + - - +
101C ILE* 3.3 11.7 - - - +
102C GLY 3.1 16.8 + - - -
67L PHE* 4.4 4.0 - - + -
68L GLU 3.5 20.4 - - - +
69L ALA* 3.3 12.7 - - - +
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Residues in contact with HIS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794B ASP 5.2 0.6 + - - -
795B GLU 3.3 20.6 + - - -
796B ARG* 3.3 34.5 - - - -
797B GLY* 3.8 5.2 + - - -
95C GLU 3.1 19.5 + - - +
96C VAL* 3.1 10.0 + - + +
98C ALA* 1.3 77.0 - - - +
100C ARG* 1.3 58.8 + - - +
102C GLY* 3.4 1.9 + - - -
103C LEU* 3.0 53.4 + - + +
216C HIS* 5.0 0.4 + - - -
218C LYS* 4.9 1.0 - - - +
69L ALA* 4.0 12.3 - - - +
70L ARG* 3.3 38.0 + - - +
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Residues in contact with ARG 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ILE* 3.7 27.1 - - - -
96C VAL* 2.9 21.0 + - + +
97C LEU* 3.8 6.3 - - + +
99C HIS* 1.3 76.4 - - - +
101C ILE* 1.3 60.1 + - + +
102C GLY 3.0 4.9 - - - -
103C LEU* 2.9 27.5 + - + +
104C VAL* 3.1 14.2 + - - +
192C LEU 2.5 30.5 + - - -
193C LEU* 3.2 19.0 + - + +
2J ILE* 3.1 30.1 - - - +
3J VAL* 2.4 40.8 + - - +
4J PRO* 4.2 4.4 - - - +
5J VAL* 3.4 20.4 - - + +
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Residues in contact with ILE 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ALA* 3.9 15.2 - - + +
83C VAL* 3.6 31.9 - - + -
97C LEU* 3.0 39.2 + - + +
98C ALA* 3.3 10.8 - - - +
100C ARG* 1.3 74.9 - - + +
102C GLY* 1.3 57.9 + - - +
104C VAL* 3.2 25.4 - - + +
134C LEU* 5.8 5.9 - - + +
136C LEU* 5.0 2.2 - - + -
167C LEU* 5.0 12.9 - - + +
193C LEU* 3.8 27.1 - - + -
204C LEU* 4.8 5.4 - - + -
206C ALA* 3.9 19.3 - - + -
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Residues in contact with GLY 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ALA* 4.3 8.5 - - - +
80C ALA* 4.0 14.7 + - - -
98C ALA 3.1 14.7 + - - -
99C HIS 3.4 4.0 + - - -
100C ARG 3.0 1.0 - - - -
101C ILE* 1.3 77.2 - - - +
103C LEU* 1.3 63.1 + - - +
104C VAL 3.3 7.2 + - - +
218C LYS* 3.2 20.9 - - - +
6J ARG* 5.3 0.3 + - - -
69L ALA* 4.0 15.7 - - - -
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795B GLU 4.6 0.2 - - - +
796B ARG* 3.9 31.4 - - + +
99C HIS* 3.0 44.3 + - + +
100C ARG* 2.9 18.4 + - + +
102C GLY* 1.3 76.1 - - - +
104C VAL* 1.3 63.4 + - - +
105C PRO* 3.3 4.0 - - - +
218C LYS* 3.7 25.6 - - + +
4J PRO* 6.0 0.2 - - + -
5J VAL* 3.4 37.4 - - + +
6J ARG* 3.4 36.1 + - + +
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Residues in contact with VAL 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ALA* 5.8 2.6 - - - +
80C ALA 5.8 0.3 + - - -
100C ARG 3.1 8.5 + - - +
101C ILE* 3.2 30.7 - - + +
102C GLY 3.6 7.8 - - - +
103C LEU* 1.3 77.8 - - - +
105C PRO* 1.3 82.4 - - + +
106C LEU* 4.5 7.6 - - + +
164C ALA* 4.5 4.5 - - + -
167C LEU* 4.4 16.2 - - + -
186C PRO* 4.1 15.7 - - + -
188C ASP 4.8 0.2 - - - +
191C ILE* 4.1 34.3 - - + -
193C LEU* 5.5 4.7 - - + -
5J VAL* 4.6 5.3 - - + +
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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