Contacts of the helix formed by residues 84 - 98 (chain t) 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 THR 84 (chain t).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105l GLU* 4.3 14.3 + - - +
49t LYS* 5.1 4.5 - - - +
50t THR* 4.8 0.9 - - - -
81t LYS* 5.9 3.6 - - - +
82t ALA 3.7 3.0 + - - +
83t MET* 1.3 77.8 - - - +
85t THR* 1.3 62.6 + - - +
86t GLY* 3.7 5.3 + - - -
87t ALA* 3.2 24.1 + - - +
88t ILE* 3.2 21.7 + - - +
113t LEU 5.7 0.7 - - - -
114t ASP* 6.0 2.0 - - - -
115t GLU* 3.6 42.4 - - + +
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Residues in contact with THR 85 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49t LYS* 3.7 2.2 + - - +
50t THR* 2.7 27.7 + - + -
84t THR* 1.3 75.6 - - - +
86t GLY* 1.3 58.9 + - - +
88t ILE* 3.1 7.0 + - - +
89t ALA* 2.9 26.7 + - - +
110t ILE* 3.6 28.7 - - + +
112t GLY* 4.4 11.7 - - - +
113t LEU 2.9 32.5 + - - -
114t ASP* 5.1 2.2 - - - +
120t ALA* 4.8 3.6 - - + +
122t TYR* 3.9 15.0 - - + -
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Residues in contact with GLY 86 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103l TYR 4.8 1.1 - - - -
104l ASN* 5.2 3.9 + - - +
84t THR* 3.4 6.2 + - - -
85t THR* 1.3 79.4 - - - +
87t ALA* 1.3 62.3 + - - +
89t ALA* 3.1 4.7 + - - +
90t ALA* 3.0 23.2 + - - +
114t ASP* 5.9 2.6 - - - +
122t TYR* 3.8 26.7 + - - -
130t TYR* 4.9 1.6 + - - -
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Residues in contact with ALA 87 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103l TYR* 3.4 34.6 + - + +
105l GLU* 4.5 8.3 - - - +
75t TYR* 5.6 0.9 - - - +
83t MET* 3.2 25.3 - - + +
84t THR* 3.2 25.9 + - - +
86t GLY* 1.3 76.2 - - - +
88t ILE* 1.3 58.2 + - - +
90t ALA* 3.4 1.7 + - - +
91t MET* 3.0 24.4 + - - +
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Residues in contact with ILE 88 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46t LEU* 3.8 23.8 - - + -
47t THR* 4.1 16.8 - - + -
50t THR* 4.2 13.7 - - + +
52t ILE* 6.0 0.2 - - + -
68t ILE* 5.2 7.0 - - + -
72t LEU* 3.6 40.6 - - + -
83t MET* 3.7 11.2 - - + +
84t THR 3.2 14.3 + - - +
85t THR* 3.1 9.0 + - - +
87t ALA* 1.3 73.9 - - - +
89t ALA* 1.3 65.5 + - - +
91t MET* 3.5 6.2 + - + +
92t LEU* 2.9 24.7 + - + +
110t ILE* 3.6 18.8 - - + -
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Residues in contact with ALA 89 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85t THR 2.9 12.2 + - - +
86t GLY 3.1 9.2 + - - +
88t ILE* 1.3 75.8 - - - +
90t ALA* 1.3 63.7 + - - +
92t LEU 3.1 2.3 + - - -
93t SER* 2.9 17.5 + - - -
110t ILE* 3.7 4.2 - - + +
122t TYR* 3.7 33.2 - - + -
124t PHE* 3.3 23.2 - - + -
130t TYR* 3.8 16.4 - - + -
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Residues in contact with ALA 90 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102l THR 3.4 19.3 - - - +
103l TYR 4.5 0.9 - - - -
104l ASN* 4.2 18.6 - - + -
57s ARG* 4.4 6.7 - - - +
86t GLY 3.0 15.4 + - - +
87t ALA 3.9 2.7 - - - +
89t ALA* 1.3 74.0 - - - +
91t MET* 1.3 66.8 + - - +
93t SER* 3.0 17.0 + - - -
94t THR* 3.1 14.4 + - - +
130t TYR* 3.9 19.4 + - + +
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Residues in contact with MET 91 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102l THR* 3.4 9.1 + - + -
103l TYR* 3.6 20.2 - - + -
68t ILE* 4.4 27.4 - - + +
71t ARG* 3.6 58.1 - - + +
72t LEU* 5.1 3.6 - - + -
83t MET* 4.0 15.7 - - + +
87t ALA 3.0 18.4 + - - +
88t ILE* 3.8 7.9 - - + +
90t ALA* 1.3 75.0 - - - +
92t LEU* 1.3 70.9 + - + +
94t THR* 2.7 23.5 + - - -
95t ILE* 3.0 25.8 + - + +
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Residues in contact with LEU 92 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52t ILE* 4.3 7.4 - - + -
64t LEU* 4.2 17.5 - - + -
68t ILE* 3.8 25.6 - - + -
88t ILE* 2.9 15.7 + - + +
89t ALA 3.4 7.9 - - - +
91t MET* 1.3 82.0 - - + +
93t SER* 1.3 63.2 + - - +
95t ILE* 3.2 7.2 + - + -
96t LEU* 3.0 45.1 + - + +
108t ASN* 3.9 21.1 - - + +
110t ILE* 4.1 10.3 - - + -
124t PHE* 3.5 35.7 - - + -
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Residues in contact with SER 93 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54s PHE* 5.6 4.9 - - - -
89t ALA 2.9 8.8 + - - -
90t ALA* 3.0 12.8 + - - -
92t LEU* 1.3 76.5 - - - +
94t THR* 1.3 61.7 + - - +
96t LEU* 3.4 2.8 + - - +
97t TYR* 3.0 23.1 + - - +
124t PHE* 3.8 3.3 - - - -
128t GLY* 2.7 34.7 + - - -
130t TYR* 3.7 26.0 - - - -
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Residues in contact with THR 94 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101l PHE* 4.0 30.1 - - + -
102l THR* 4.2 21.6 - - + +
54s PHE* 4.9 8.9 - - + -
57s ARG* 6.1 2.0 - - - +
71t ARG* 4.4 4.3 + - - -
90t ALA 3.1 10.8 + - - +
91t MET* 2.7 21.3 + - - -
93t SER* 1.3 75.9 - - - +
95t ILE* 1.3 71.1 + - - +
97t TYR* 3.2 6.2 + - - +
98t SER* 3.0 23.4 + - - -
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Residues in contact with ILE 95 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64t LEU* 4.0 23.6 - - + -
67t ILE* 4.0 28.5 - - + -
68t ILE* 4.9 5.4 - - + -
71t ARG* 3.9 25.8 - - + +
91t MET* 3.0 40.4 + - + +
92t LEU* 3.2 6.7 + - + +
94t THR* 1.3 84.0 + - - +
96t LEU* 1.3 62.1 + - - +
98t SER* 2.8 25.5 + - - +
99t ARG 4.0 1.2 + - - -
104t TYR* 4.0 14.6 - - + +
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Residues in contact with LEU 96 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64t LEU* 4.0 24.9 - - + -
92t LEU* 3.0 35.9 + - + +
93t SER 3.7 1.3 - - - +
95t ILE* 1.3 77.2 - - - +
97t TYR* 1.3 62.3 + - - +
99t ARG* 3.4 19.1 + - - +
100t ARG* 4.6 0.5 - - - -
103t PRO* 5.5 0.9 - - - +
104t TYR* 3.8 27.6 - - + +
106t VAL* 5.3 1.1 - - + -
108t ASN* 4.1 11.4 - - - +
124t PHE* 4.0 9.4 - - + -
125t ASP 3.6 22.2 - - - +
126t PRO* 3.7 21.8 - - + +
127t VAL* 3.9 5.3 - - - +
128t GLY* 3.7 15.0 - - - +
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Residues in contact with TYR 97 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50s ALA* 4.1 9.6 - - + -
51s ASP* 2.8 28.9 + - - -
54s PHE* 2.9 69.5 - + + -
55s TRP* 3.0 25.0 + + - -
90s TYR* 6.3 1.6 - + - -
95s LEU* 3.6 8.5 - - - +
93t SER* 3.0 16.0 + - - +
94t THR 3.2 2.0 + - - +
96t LEU* 1.3 74.1 - - - +
98t SER* 1.3 62.2 + - - +
99t ARG 3.0 6.1 - - - -
100t ARG* 3.0 36.7 + - + +
101t PHE* 5.6 1.5 - + - -
127t VAL* 3.3 20.4 + - + +
128t GLY 5.9 0.2 - - - -
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Residues in contact with SER 98 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54s PHE* 5.7 0.9 - - - -
94t THR 3.0 13.2 + - - -
95t ILE* 2.8 23.5 + - - +
96t LEU 3.3 0.2 - - - -
97t TYR* 1.3 78.4 - - - +
99t ARG* 1.3 64.6 + - - +
100t ARG* 3.3 2.3 + - - -
101t PHE* 6.0 1.6 - - - -
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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