Contacts of the helix formed by residues 93 - 111 (chain t) in PDB entry 3J9X
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 GLY 93 (chain t).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92t SER* 1.3 76.8 - - - +
94t PRO* 1.3 68.1 - - - -
95t ALA 3.3 1.8 - - - -
96t LEU* 2.8 29.1 + - - +
97t VAL* 3.2 15.8 + - - +
133t VAL* 4.5 10.5 - - - -
64v THR* 4.5 0.9 - - - -
65v GLN* 5.3 2.2 - - - -
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Residues in contact with PRO 94 (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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93t GLY* 1.3 84.1 - - - -
95t ALA* 1.3 63.9 + - - +
97t VAL* 3.0 6.2 + - - +
98t ASN* 2.9 27.0 + - - +
133t VAL* 3.8 25.3 - - + -
64v THR* 3.3 15.5 - - + +
65v GLN* 3.4 39.9 - - - +
66v TYR 4.7 0.4 - - - -
67v GLY* 3.9 11.4 - - - -
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Residues in contact with ALA 95 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90t ILE* 3.6 22.8 - - + +
93t GLY 3.1 0.4 + - - -
94t PRO* 1.3 79.3 - - - +
96t LEU* 1.3 56.7 + - - +
98t ASN* 3.3 2.0 + - - +
99t MET* 3.0 24.1 + - - +
64v THR* 3.2 19.2 + - + +
67v GLY* 3.5 16.1 - - - -
68v ILE 3.6 21.8 - - - +
69v THR* 3.4 13.8 - - + +
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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
----------------------------------------------------------
83t VAL* 4.5 3.8 - - + +
86t ALA* 3.8 20.4 - - + +
87t LEU* 3.6 52.5 - - + +
90t ILE* 4.0 5.1 - - + +
91t GLY 3.4 12.3 + - - +
92t SER* 3.8 11.4 - - - -
93t GLY 2.8 15.6 + - - +
95t ALA* 1.3 72.0 - - - +
97t VAL* 1.3 62.4 + - + +
99t MET* 3.1 6.3 + - + +
100t ILE* 2.8 49.9 + - + +
126t THR* 4.8 10.1 - - + -
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Residues in contact with VAL 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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93t GLY 3.9 9.2 - - - +
94t PRO 3.0 8.4 + - - +
96t LEU* 1.3 80.1 - - + +
98t ASN* 1.3 66.7 + - - +
100t ILE* 3.2 5.5 + - + +
101t ASN* 2.9 28.4 + - - +
130t THR* 3.5 21.5 + - - +
131t GLY 3.7 25.8 - - - +
132t TYR* 4.2 7.6 - - - +
133t VAL* 3.8 33.7 - - + +
134t SER 5.2 0.7 - - - +
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Residues in contact with ASN 98 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109s SER 3.5 22.3 - - - +
110s ALA* 3.6 4.0 - - - +
112s ASN* 5.1 9.5 - - - +
94t PRO* 2.9 14.4 + - - +
95t ALA* 3.4 8.5 - - - +
96t LEU 3.2 0.2 - - - -
97t VAL* 1.3 79.5 - - - +
99t MET* 1.3 64.5 + - - +
101t ASN* 3.5 9.1 + - - +
102t GLY 3.3 13.2 + - - -
67v GLY* 3.1 35.4 + - - -
69v THR* 4.4 7.2 - - + -
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Residues in contact with MET 99 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717 A 4.1 13.5 - - - +
106s TYR* 4.6 12.6 - - - +
110s ALA* 3.9 20.4 + - - +
111s PHE* 3.7 31.2 - - + -
82t LYS* 5.9 2.0 - - - -
86t ALA* 3.8 24.0 - - + -
90t ILE* 3.8 22.7 - - + -
95t ALA 3.0 13.8 + - - +
96t LEU* 3.3 12.6 - - + +
98t ASN* 1.3 75.9 - - - +
100t ILE* 1.3 61.1 + - + +
102t GLY* 3.2 3.3 + - - -
103t LEU* 2.9 34.3 + - + +
69v THR* 4.7 5.2 - - + -
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Residues in contact with ILE 100 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79t PHE* 5.1 1.1 - - + -
83t VAL* 4.3 22.7 - - + -
96t LEU* 2.8 48.6 + - + +
97t VAL* 3.8 3.6 - - + +
99t MET* 1.3 75.1 - - + +
101t ASN* 1.3 58.0 + - - +
103t LEU* 4.1 6.7 - - + -
104t LYS* 2.7 33.7 + - + +
122t VAL* 4.3 20.6 - - + -
126t THR* 4.1 23.8 - - + -
130t THR* 3.6 34.1 - - + +
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Residues in contact with ASN 101 (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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109s SER* 4.2 8.4 + - - +
97t VAL* 2.9 22.8 + - - +
98t ASN* 3.7 9.9 + - - +
99t MET 3.2 0.2 - - - -
100t ILE* 1.3 76.7 - - - +
102t GLY* 1.3 61.6 + - - +
104t LYS* 3.8 3.2 - - - +
105t GLY* 3.2 19.6 + - - -
130t THR* 2.5 31.5 + - - +
131t GLY* 2.9 33.2 + - - -
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Residues in contact with GLY 102 (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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105s GLY 4.2 2.8 - - - -
106s TYR* 3.7 11.7 + - - -
109s SER* 2.9 25.3 + - - -
110s ALA* 4.1 10.8 - - - -
98t ASN 3.3 4.8 + - - -
99t MET 3.2 6.0 + - - -
101t ASN* 1.3 76.8 - - - +
103t LEU* 1.3 60.4 + - - +
105t GLY* 3.4 1.8 + - - -
106t TYR* 2.9 29.6 + - - +
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Residues in contact with LEU 103 (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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106s TYR* 4.0 12.0 - - + -
79t PHE* 3.7 10.3 - - + -
82t LYS* 3.5 50.5 - - + +
83t VAL* 3.7 35.0 - - + +
99t MET* 2.9 24.7 + - + +
100t ILE* 3.6 7.9 - - + +
102t GLY* 1.3 75.1 - - - +
104t LYS* 1.3 64.7 + - - +
106t TYR* 3.2 9.1 - - + +
107t TYR* 3.0 38.8 + - + -
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Residues in contact with LYS 104 (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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79t PHE* 3.8 17.7 - - + -
100t ILE* 2.7 23.1 + - + +
101t ASN* 3.8 4.0 - - - +
103t LEU* 1.3 73.4 - - - +
105t GLY* 1.3 65.2 + - - +
107t TYR* 3.1 4.7 + - - +
108t ILE* 3.0 46.7 + - + +
115t PRO* 4.4 13.5 - - - +
118t LEU* 4.0 13.5 - - + +
119t ASP* 2.7 38.7 + - - +
122t VAL* 6.0 1.6 - - + -
130t THR* 4.3 19.1 - - + +
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Residues in contact with GLY 105 (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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102s GLY 5.0 0.9 - - - -
105s GLY* 5.9 3.8 - - - -
106s TYR 5.7 0.2 - - - -
101t ASN 3.2 12.3 + - - -
102t GLY* 3.8 2.7 - - - -
104t LYS* 1.3 78.3 - - - +
106t TYR* 1.3 62.6 + - - +
108t ILE* 3.2 12.0 + - - +
109t SER* 3.1 28.8 + - - -
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Residues in contact with TYR 106 (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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2688 T 4.2 0.2 + - - -
2698 A 3.3 15.4 + - - -
82s LYS* 2.7 34.6 + - - -
99s MET* 4.7 3.7 - - - -
102s GLY 3.5 27.7 + - - -
103s LEU* 4.1 14.4 - - + -
106s TYR* 3.7 25.7 - + + +
82t LYS* 5.0 5.8 - - - -
102t GLY 2.9 18.0 + - - +
103t LEU* 3.2 13.7 - - + +
105t GLY* 1.3 74.9 - - - +
107t TYR* 1.3 81.4 + + - +
110t ALA* 2.8 45.9 + - + +
111t PHE* 3.7 28.2 - + - -
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Residues in contact with TYR 107 (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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2688 T 4.4 6.9 + - + +
2698 A 3.4 25.1 + - - -
71q PRO* 6.5 1.3 - - + -
75t ILE* 3.5 37.9 - - + -
78t GLY* 3.5 4.9 - - - -
79t PHE* 3.5 38.8 + + + -
82t LYS* 4.6 4.3 - - + -
103t LEU* 3.0 30.5 + - + +
104t LYS 3.8 5.4 - - - +
106t TYR* 1.3 96.1 - + - +
108t ILE* 1.3 66.6 + - - +
111t PHE* 3.0 44.8 + + - -
113t ALA* 3.1 22.1 + - + +
118t LEU* 4.4 2.7 - - + -
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Residues in contact with ILE 108 (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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104t LYS* 3.0 46.4 + - + +
105t GLY* 3.6 11.4 - - - +
107t TYR* 1.3 77.0 - - - +
109t SER* 1.3 61.4 + - - +
112t ASN* 3.0 26.0 - - - +
113t ALA 3.4 16.1 + - - +
115t PRO* 3.9 24.5 - - + -
118t LEU* 3.3 16.6 - - + -
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Residues in contact with SER 109 (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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98s ASN* 3.5 18.4 - - - +
101s ASN* 4.2 6.5 - - - -
102s GLY* 3.0 28.7 + - - -
105t GLY 3.1 11.1 + - - -
108t ILE* 1.3 82.4 - - - +
110t ALA* 1.3 64.3 + - - +
111t PHE 3.4 0.4 - - - -
112t ASN* 4.0 10.6 - - - +
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Residues in contact with ALA 110 (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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69q THR* 2.6 34.3 + - - +
98s ASN* 3.7 13.8 - - - +
99s MET* 4.2 15.6 - - - +
102s GLY* 4.1 11.0 - - - -
106t TYR* 2.8 36.0 + - + +
109t SER* 1.3 77.0 + - - +
111t PHE* 1.3 69.0 + - + +
112t ASN* 3.6 1.4 - - - -
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Residues in contact with PHE 111 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2688 T 3.6 38.4 - - - -
69q THR* 3.4 17.3 - - - +
70q GLY* 3.6 18.6 - - - -
71q PRO* 4.6 3.4 - - + -
72q ASN* 3.2 18.9 + - - +
82s LYS* 6.1 0.2 - - - -
99s MET* 3.8 23.6 - - + -
75t ILE* 4.6 13.8 - - + +
106t TYR* 3.7 37.2 - + - -
107t TYR* 3.0 45.9 + + + +
110t ALA* 1.3 80.5 - - + +
112t ASN* 1.3 74.9 + - - +
113t ALA* 3.2 2.3 + - - +
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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
------------------------------------------------------------
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