Contacts of the helix formed by residues 84 - 102 (chain g) 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 g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G ARG* 5.6 4.0 - - - +
48g SER* 5.3 0.2 - - - -
49g THR* 4.5 0.2 - - - -
82g SER 3.2 5.7 + - - -
83g TYR* 1.3 76.4 - - - +
85g PRO* 1.3 74.4 - - - +
86g ARG* 3.6 10.4 + - - +
87g ALA* 3.1 32.5 + - - +
88g ILE* 3.1 14.8 + - - +
116g ALA* 5.2 7.0 - - - -
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Residues in contact with PRO 85 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48g SER* 3.6 25.4 - - - +
49g THR* 3.9 18.6 - - + -
83g TYR 4.2 0.7 - - - +
84g SER* 1.3 89.0 - - - +
86g ARG* 1.4 63.5 + - + +
88g ILE* 3.2 5.8 + - + +
89g HIS* 3.0 23.9 + - - +
112g ILE* 4.1 4.2 - - + +
114g GLY* 3.7 17.3 - - - +
115g TYR 4.2 0.9 - - - +
116g ALA* 4.1 20.0 - - + +
121g PHE* 3.7 31.6 - - + -
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Residues in contact with ARG 86 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G PHE 4.7 1.6 - - - -
100G ASP* 3.9 28.1 + - + +
84g SER* 3.2 9.7 + - - +
85g PRO* 1.4 75.7 - - + +
87g ALA* 1.3 57.3 + - - +
89g HIS* 3.5 4.2 + - - +
90g SER* 2.9 28.6 + - - -
121g PHE* 3.4 42.4 - - + -
133g GLU* 3.5 18.7 + - - -
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Residues in contact with ALA 87 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G PHE* 3.6 40.5 + - + +
101G ARG* 4.6 9.2 - - + +
83g TYR* 4.3 9.6 - - + -
84g SER* 3.1 27.0 + - - +
86g ARG* 1.3 77.5 - - - +
88g ILE* 1.3 66.2 + - - +
89g HIS 3.2 0.2 - - - -
90g SER* 3.3 2.3 + - - -
91g TRP* 3.0 24.1 + - - +
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Residues in contact with ILE 88 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G PHE* 6.0 0.2 - - + -
45g VAL* 4.1 23.3 - - + -
49g THR* 4.4 13.0 - - + +
51g LEU* 6.0 0.4 - - + -
67g LEU* 4.0 38.6 - - + -
70g MET* 5.4 4.0 - - + -
71g VAL* 4.8 1.8 - - + -
83g TYR* 3.6 35.4 - - + -
84g SER 3.1 19.4 + - - +
85g PRO* 3.6 8.7 - - + +
87g ALA* 1.3 76.3 - - - +
89g HIS* 1.3 58.4 + - - +
91g TRP* 3.3 5.8 + - - +
92g LEU* 3.0 29.2 + - + +
112g ILE* 4.0 17.7 - - + -
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Residues in contact with HIS 89 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85g PRO 3.0 16.7 + - - +
86g ARG 3.5 5.4 + - - +
88g ILE* 1.3 76.4 - - - +
90g SER* 1.3 56.3 + - - +
92g LEU* 3.5 1.6 + - - +
93g THR* 2.7 39.2 + - - -
112g ILE* 3.5 15.3 - - + -
121g PHE* 3.6 22.0 - + + -
123g GLY* 3.7 20.1 - - - -
124g TYR 3.3 25.3 + - - -
125g VAL* 3.4 18.3 - - + +
131g ALA* 3.8 20.9 - - + -
132g TYR* 4.0 14.1 - - - -
133g GLU* 5.0 4.4 + - + +
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Residues in contact with SER 90 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G PHE 4.1 0.2 + - - -
98G VAL 2.3 30.9 + - - +
99G PHE 3.5 15.3 - - - -
100G ASP* 4.5 4.7 - - - -
66f LYS* 3.6 17.3 + - - +
86g ARG 2.9 18.2 + - - -
87g ALA 3.3 4.9 + - - -
89g HIS* 1.3 77.5 - - - +
91g TRP* 1.3 64.7 + - - +
93g THR* 3.2 8.1 + - - -
94g ARG* 2.9 23.7 + - - +
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Residues in contact with TRP 91 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G VAL* 3.3 31.4 - - + -
99G PHE* 3.8 22.6 - + + -
63g LEU* 4.7 10.3 - - + -
66g VAL* 3.6 31.0 - - + -
67g LEU* 3.8 32.3 - - + -
70g MET* 3.4 27.4 - - + -
87g ALA 3.0 17.1 + - - +
88g ILE* 3.6 4.9 - - - +
90g SER* 1.3 78.7 - - - +
92g LEU* 1.3 86.1 + - + +
94g ARG* 3.2 5.0 + - + +
95g ALA* 2.9 36.2 + - + +
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Residues in contact with LEU 92 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51g LEU* 4.5 6.1 - - + -
63g LEU* 4.0 27.6 - - + -
67g LEU* 4.5 13.0 - - + -
88g ILE 3.0 17.5 + - - +
89g HIS* 3.8 4.0 - - - +
91g TRP* 1.3 101.4 - - + +
93g THR* 1.3 60.3 + - - +
95g ALA* 3.3 3.6 + - + +
96g MET* 3.0 30.3 + - + +
110g MET* 3.5 40.6 - - + -
112g ILE* 3.8 22.7 - - + -
125g VAL* 4.2 7.4 - - + -
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Residues in contact with THR 93 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62f LEU* 5.0 2.7 - - + -
89g HIS* 2.7 23.9 + - - -
90g SER* 3.2 11.2 + - - -
92g LEU* 1.3 77.9 - - - +
94g ARG* 1.3 89.4 + - - +
96g MET* 3.3 2.1 + - - +
97g TYR* 2.9 21.7 + - - +
125g VAL* 3.8 13.5 - - - +
129g GLY* 3.7 23.0 - - - +
131g ALA* 3.4 25.5 - - + +
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Residues in contact with ARG 94 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G PHE* 3.7 37.2 - - + +
98G VAL* 4.6 11.9 - - + +
59f GLY 4.0 2.4 + - - -
62f LEU* 4.0 16.8 - - - +
63f THR* 2.3 50.6 + - - +
66f LYS* 4.2 26.6 - - - +
90g SER* 2.9 14.2 + - - +
91g TRP* 3.7 8.5 - - - +
93g THR* 1.3 104.8 - - - +
95g ALA* 1.3 58.3 + - - +
97g TYR* 3.4 16.2 + - - +
98g SER* 2.9 29.3 + - - -
129g GLY 5.5 0.4 + - - -
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Residues in contact with ALA 95 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63g LEU* 5.0 11.4 - - + -
91g TRP* 2.9 29.9 + - + +
92g LEU* 3.5 11.9 - - - +
93g THR 3.2 0.2 - - - -
94g ARG* 1.3 75.1 - - - +
96g MET* 1.3 69.5 + - + +
98g SER* 3.1 7.0 + - - -
99g ARG* 3.0 28.7 + - + +
106g LEU* 5.3 2.5 - - + -
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Residues in contact with MET 96 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63g LEU* 4.0 7.4 - - - -
92g LEU* 3.0 17.1 + - - +
93g THR 3.8 3.6 - - - +
95g ALA* 1.3 75.8 - - - +
97g TYR* 1.3 56.9 + - - +
99g ARG* 3.5 4.6 + - - +
100g ARG* 2.9 30.3 + - - +
105g PRO* 5.3 0.5 - - - +
106g LEU* 3.0 58.1 - - + +
108g ASN* 3.7 7.2 - - + +
110g MET* 3.6 27.1 - - + -
125g VAL* 3.7 11.2 - - + -
126g ASP 3.4 21.3 - - - +
127g MET* 3.7 21.2 - - - +
129g GLY* 4.4 3.8 - - - +
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Residues in contact with TYR 97 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59f GLY* 3.6 13.9 - - - -
60f ASP* 3.0 26.2 + - - -
63f THR* 2.9 45.3 - - + +
99f ARG* 2.7 27.4 + - - -
104f TYR* 3.7 2.6 - - - -
93g THR 2.9 17.2 + - - +
94g ARG* 3.7 17.0 - - - +
95g ALA 3.2 0.2 - - - -
96g MET* 1.3 78.7 - - - +
98g SER* 1.3 59.7 + - - +
100g ARG* 3.3 19.9 + - - +
101g SER* 2.7 44.0 + - - -
128g LEU 3.9 14.8 - - - -
129g GLY* 4.2 8.9 - - - -
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Residues in contact with SER 98 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94g ARG 2.9 15.1 + - - -
95g ALA* 3.1 10.7 + - - -
97g TYR* 1.3 81.4 - - - +
99g ARG* 1.3 64.4 + - - +
101g SER* 3.2 7.8 + - - -
102g LYS* 3.0 45.2 + - - +
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Residues in contact with ARG 99 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88a TYR* 3.3 27.7 + - - -
1g THR* 4.2 3.6 + - - +
62g TYR* 4.8 10.5 + - - -
95g ALA* 3.0 16.3 + - + +
96g MET 3.9 3.1 - - - +
98g SER* 1.3 81.4 - - - +
100g ARG* 1.3 62.7 + - - +
102g LYS* 3.1 22.3 + - - +
104g ASN* 2.4 92.1 + - - +
105g PRO* 3.7 17.0 + - + -
106g LEU* 3.5 29.2 - - + +
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Residues in contact with ARG 100 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2f PHE* 3.9 14.6 - - + -
4f PRO* 3.1 21.1 + - + +
5f TYR* 3.7 14.5 - - - -
57f PHE* 3.2 25.4 - - - -
60f ASP* 3.0 30.0 + - - -
99f ARG* 4.4 5.5 - - - +
102f PHE* 4.0 19.8 - - - -
103f PRO 5.0 0.2 + - - -
96g MET 2.9 18.2 + - - +
97g TYR* 3.4 15.1 + - - +
99g ARG* 1.3 75.8 - - - +
101g SER* 1.3 78.7 + - - +
103g MET* 3.1 23.7 + - - +
105g PRO* 4.2 11.3 - - - +
127g MET 3.6 10.8 - - - +
128g LEU* 3.9 33.0 - - + +
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Residues in contact with SER 101 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99f ARG* 4.3 8.9 + - - -
102f PHE* 3.6 25.3 - - - -
97g TYR* 2.7 36.1 + - - -
98g SER* 3.2 8.0 + - - -
100g ARG* 1.3 99.0 + - - +
102g LYS* 1.3 58.0 + - - +
103g MET* 3.2 2.3 - - - +
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Residues in contact with LYS 102 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98g SER* 3.0 32.9 + - - +
99g ARG* 3.1 20.9 + - - +
101g SER* 1.3 77.2 - - - +
103g MET* 1.3 68.8 + - - +
104g ASN* 3.0 12.9 + - + +
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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