Contacts of the helix formed by residues 84 - 102 (chain u) in PDB entry 5GJQ
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 84 (chain u).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101m ARG* 5.5 3.8 - - - +
82u SER 3.2 6.2 + - - -
83u TYR* 1.3 75.0 - - - +
85u PRO* 1.3 76.1 - - - +
86u ARG* 3.7 9.8 + - - +
87u ALA* 3.1 32.2 + - - +
88u ILE* 3.1 13.1 + - - +
116u ALA* 5.2 6.1 - - - -
117u ASP* 6.0 1.8 - - - -
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Residues in contact with PRO 85 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48u SER* 3.6 24.2 - - - +
49u THR* 4.0 15.5 - - + -
83u TYR 4.3 2.0 - - - +
84u SER* 1.3 91.2 - - - +
86u ARG* 1.3 65.6 + - + +
88u ILE* 3.1 6.9 + - + +
89u HIS* 3.0 22.2 + - - +
112u ILE* 4.3 3.1 - - + +
114u GLY* 3.8 14.6 - - - -
115u TYR 4.2 1.8 - - - +
116u ALA* 4.0 19.7 - - + +
121u PHE* 3.7 33.3 - - + -
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Residues in contact with ARG 86 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99m PHE 4.4 0.8 - - - +
100m ASP* 3.9 22.9 + - + +
84u SER* 3.2 8.4 - - - +
85u PRO* 1.3 78.6 - - + +
87u ALA* 1.3 57.9 + - - +
89u HIS* 3.4 4.3 + - - +
90u SER* 3.0 27.4 + - - -
121u PHE* 3.3 43.1 - - + -
133u GLU* 3.6 18.1 + - - +
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Residues in contact with ALA 87 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99m PHE* 3.3 37.7 - - + +
101m ARG* 4.3 11.2 - - + +
83u TYR* 4.2 9.9 - - + -
84u SER* 3.1 27.8 + - - +
86u ARG* 1.3 78.8 - - - +
88u ILE* 1.3 65.8 + - - +
90u SER* 3.3 3.5 + - - -
91u TRP* 3.0 23.4 + - - +
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Residues in contact with ILE 88 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99m PHE* 5.4 0.2 - - + -
45u VAL* 5.0 8.3 - - + -
46u ASN* 5.1 1.1 - - - +
49u THR* 4.3 18.8 - - + +
67u LEU* 3.9 41.3 - - + -
70u MET* 5.2 4.7 - - + -
71u VAL* 5.4 1.3 - - + -
83u TYR* 3.5 35.9 - - + -
84u SER 3.4 14.8 - - - +
85u PRO* 3.1 7.8 + - + +
87u ALA* 1.3 77.1 - - - +
89u HIS* 1.3 59.0 + - - +
91u TRP* 3.3 5.4 + - - +
92u LEU* 3.0 29.5 + - + +
112u ILE* 4.0 20.0 - - + -
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Residues in contact with HIS 89 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85u PRO 3.0 13.2 + - - +
86u ARG 3.5 9.3 + - - +
87u ALA 3.1 0.2 - - - -
88u ILE* 1.3 74.5 - - - +
90u SER* 1.3 61.6 + - - +
92u LEU* 3.5 2.3 + - - +
93u THR* 2.7 37.2 + - - -
112u ILE* 3.6 14.8 - - + +
121u PHE* 3.6 18.8 - + + -
123u GLY* 3.8 19.7 - - - -
124u TYR 3.3 24.7 + - - -
125u VAL* 3.4 19.0 - - + +
131u ALA* 3.7 23.3 - - + -
132u TYR* 3.7 14.3 + - - -
133u GLU* 4.7 6.8 + - + +
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Residues in contact with SER 90 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97m PHE 4.0 5.5 + - - -
98m VAL 2.8 25.2 + - - +
99m PHE 3.5 13.9 - - - -
100m ASP* 3.6 13.0 + - - +
66t LYS* 4.1 13.5 + - - +
86u ARG 3.0 14.3 + - - -
87u ALA 3.5 7.4 - - - -
89u HIS* 1.3 80.9 - - - +
91u TRP* 1.3 63.6 + - - +
93u THR* 3.2 7.8 + - - -
94u ARG* 3.0 23.0 + - - +
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Residues in contact with TRP 91 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98m VAL* 3.0 40.9 - - + +
99m PHE* 3.9 18.8 - + + -
63u LEU* 4.9 9.2 - - + -
66u VAL* 3.6 32.5 - - + -
67u LEU* 3.9 30.7 - - + -
70u MET* 3.3 25.8 - - + -
87u ALA 3.0 13.8 + - - +
88u ILE* 3.7 5.4 - - - +
90u SER* 1.3 81.6 - - - +
92u LEU* 1.3 96.6 + - + +
94u ARG* 3.2 5.3 + - + +
95u ALA* 3.0 29.4 + - + +
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Residues in contact with LEU 92 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51u LEU* 4.3 11.4 - - + -
63u LEU* 4.0 30.5 - - + -
67u LEU* 5.0 4.7 - - + -
88u ILE* 3.0 17.1 + - + +
89u HIS 3.7 4.9 - - - +
91u TRP* 1.3 100.9 - - + +
93u THR* 1.3 62.2 + - - +
95u ALA* 3.2 3.7 + - + +
96u MET* 3.0 29.1 + - - +
110u MET* 3.6 37.7 - - + -
112u ILE* 3.7 24.0 - - + -
125u VAL* 4.1 9.6 - - + -
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Residues in contact with THR 93 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62t LEU* 4.6 3.8 - - + -
66t LYS* 5.2 1.1 - - - +
89u HIS* 2.7 23.6 + - - -
90u SER* 3.4 10.1 - - - -
92u LEU* 1.3 76.4 - - - +
94u ARG* 1.3 88.3 + - - +
96u MET* 3.3 2.8 + - - +
97u TYR* 3.0 21.3 + - - +
125u VAL* 3.9 13.9 - - - +
129u GLY* 3.5 26.8 - - - +
131u ALA* 3.5 25.5 - - + +
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Residues in contact with ARG 94 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97m PHE* 3.8 46.5 - - + +
98m VAL* 4.4 11.9 - - + +
59t GLY 4.0 2.4 + - - -
62t LEU* 3.8 11.7 - - - +
63t THR* 2.2 50.0 + - - +
66t LYS* 3.2 27.2 - - - +
90u SER* 3.0 12.9 + - - +
91u TRP* 3.6 9.6 - - + +
93u THR* 1.3 102.3 - - - +
95u ALA* 1.3 62.2 + - - +
97u TYR* 3.5 16.0 + - - +
98u SER* 3.0 24.8 + - - -
129u GLY 5.8 0.2 + - - -
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Residues in contact with ALA 95 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63u LEU* 5.0 15.3 - - + -
91u TRP* 3.0 24.0 + - + +
92u LEU* 3.4 11.7 - - - +
94u ARG* 1.3 74.5 - - - +
96u MET* 1.3 69.2 + - + +
98u SER* 3.1 7.7 + - - -
99u ARG* 3.1 28.4 + - + +
106u LEU* 5.3 3.4 - - + -
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Residues in contact with MET 96 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63u LEU* 4.0 7.4 - - - -
92u LEU* 3.0 17.8 + - - +
93u THR 3.7 4.0 - - - +
95u ALA* 1.3 80.3 - - - +
97u TYR* 1.3 62.9 + - - +
99u ARG* 3.4 5.6 + - - +
100u ARG* 3.0 23.4 + - - +
106u LEU* 3.1 54.6 + - + +
108u ASN* 3.8 7.6 - - + +
110u MET* 3.6 26.7 - - + -
125u VAL* 3.6 11.9 - - + -
126u ASP 3.4 26.5 - - - +
127u MET* 3.5 16.8 - - - +
129u GLY* 4.4 3.4 - - - +
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Residues in contact with TYR 97 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57t PHE* 4.9 0.4 - + - -
59t GLY* 3.7 13.9 - - - -
60t ASP* 3.2 24.6 + - - -
63t THR* 3.0 37.6 - - + +
99t ARG* 2.6 29.1 + - - -
104t TYR* 3.6 10.2 - - - -
93u THR 3.0 17.3 + - - +
94u ARG* 3.8 15.5 - - - +
96u MET* 1.3 76.6 - - - +
98u SER* 1.3 67.7 + - - +
100u ARG* 3.2 12.0 + - - +
101u SER* 2.7 45.7 + - - -
128u LEU 3.8 22.0 - - - +
129u GLY* 4.4 4.4 - - - -
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Residues in contact with SER 98 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94u ARG 3.0 18.1 + - - -
95u ALA* 3.1 7.8 + - - -
97u TYR* 1.3 81.9 - - - +
99u ARG* 1.3 65.6 + - - +
101u SER* 3.2 7.2 + - - -
102u LYS* 3.2 43.9 + - - +
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Residues in contact with ARG 99 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88o TYR* 3.2 28.3 + - - -
1u THR* 4.2 3.0 + - - +
59u ASP* 5.1 0.2 + - - -
62u TYR* 4.9 8.5 + - - -
95u ALA* 3.1 14.2 + - + +
96u MET 3.8 3.8 - - - +
98u SER* 1.3 81.0 - - - +
100u ARG* 1.3 62.8 + - - +
102u LYS* 3.2 29.8 + - - +
104u ASN* 2.3 90.3 + - - +
105u PRO* 3.7 16.2 + - + -
106u LEU* 3.4 29.2 - - + +
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Residues in contact with ARG 100 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2t PHE* 4.0 7.9 - - + -
4t PRO* 3.1 27.6 + - + +
5t TYR* 3.4 23.6 - - - -
57t PHE* 4.3 2.7 - - - -
60t ASP* 3.2 24.2 + - - -
99t ARG* 4.1 5.9 - - - +
102t PHE* 3.2 37.5 - - - -
103t PRO 4.6 0.8 + - - -
96u MET 3.0 18.3 + - - +
97u TYR* 3.4 15.4 + - - +
99u ARG* 1.3 77.9 - - - +
101u SER* 1.3 77.1 + - - +
103u MET* 3.1 19.4 + - - -
105u PRO* 4.2 11.4 - - - +
127u MET 3.8 11.0 - - - +
128u LEU* 3.6 39.0 - - + +
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Residues in contact with SER 101 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99t ARG* 4.6 9.4 - - - -
102t PHE* 3.1 29.6 - - - -
97u TYR* 2.7 36.0 + - - -
98u SER* 3.6 7.2 - - - -
99u ARG 3.2 0.2 - - - -
100u ARG* 1.3 99.8 + - - +
102u LYS* 1.3 58.7 + - - +
103u MET* 3.2 2.1 - - - +
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Residues in contact with LYS 102 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98u SER* 3.2 29.9 + - - +
99u ARG* 3.2 30.4 + - - +
101u SER* 1.3 79.1 - - - +
103u MET* 1.3 65.8 + - - +
104u ASN* 3.0 17.8 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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