Contacts of the strand formed by residues 107 - 115 (chain O) in PDB entry 2GTL
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 LYS 107 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105O GLY 3.7 8.3 + - - +
106O ASP* 1.3 79.4 - - - +
108O PHE* 1.3 64.7 + - - +
109O ILE* 6.2 0.2 - - + -
126O THR* 4.8 13.4 - - + +
127O LEU 3.6 4.3 - - - +
128O ALA* 4.2 23.6 - - + -
149O GLU* 4.5 13.0 + - - -
220O ARG* 3.7 7.5 - - - +
221O LYS* 2.8 42.9 + - + +
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Residues in contact with PHE 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102O THR* 3.5 29.4 - - + -
106O ASP* 4.5 4.3 - - + -
107O LYS* 1.3 78.7 - - - +
109O ILE* 1.3 63.9 + - - +
125O MET 3.8 0.7 - - - +
126O THR* 3.5 1.6 - - - -
127O LEU* 2.7 49.7 + - + +
129O PHE* 3.8 18.8 - + - -
192O PHE* 4.1 8.5 - + - -
197O PHE 4.4 0.4 - - - -
198O ASP 4.4 8.1 - - - -
200O PHE* 3.8 25.6 - + + -
218O PHE* 4.0 10.7 - - + -
219O HIS 3.2 8.5 - - - -
220O ARG* 3.3 72.9 - - + -
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Residues in contact with ILE 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108O PHE* 1.3 73.4 - - - +
110O GLY* 1.3 65.5 + - - +
111O ASP* 3.8 16.9 - - - +
124O HIS* 4.7 14.8 - - + +
125O MET 5.7 0.2 - - - +
126O THR* 2.9 43.3 - - + +
217O ILE 3.5 1.9 - - - +
218O PHE* 3.4 1.1 - - - -
219O HIS* 2.8 40.5 + - + +
221O LYS* 4.2 19.7 - - + +
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Residues in contact with GLY 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109O ILE* 1.3 74.3 - - - +
111O ASP* 1.3 63.9 + - - -
112O VAL 3.9 0.2 + - - -
124O HIS* 3.2 10.9 + - - +
125O MET 2.9 38.9 + - - -
216O PHE* 4.0 5.2 - - - -
217O ILE 3.3 8.1 - - - -
218O PHE* 3.7 21.6 - - - -
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Residues in contact with ASP 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M VAL* 4.1 21.3 - - + +
90M ARG* 5.9 3.4 - - + -
109O ILE* 3.8 18.9 - - - +
110O GLY* 1.3 76.5 - - - -
112O VAL* 1.3 68.4 + - - +
124O HIS* 3.5 26.3 - - + +
216O PHE* 3.3 2.0 - - - -
217O ILE* 3.0 36.8 + - + +
219O HIS* 4.2 12.9 - - - -
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Residues in contact with VAL 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73M VAL* 4.7 2.8 - - - +
90M ARG* 3.2 35.1 + - - +
111O ASP* 1.3 77.7 - - - +
113O CYS* 1.3 72.5 + - - +
114O PHE 3.7 10.5 - - - +
115O ASP* 3.7 19.3 - - + +
121O ARG 5.9 0.2 - - - -
122O PRO 3.4 14.6 - - - +
123O GLU* 3.2 27.1 + - - +
216O PHE* 3.4 43.4 - - + -
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Residues in contact with CYS 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M VAL* 4.5 16.8 - - + -
74M PRO* 4.6 14.4 - - + +
75M GLU* 4.8 17.2 - - - +
90M ARG* 3.3 16.4 + - - +
111O ASP 4.5 1.6 - - - +
112O VAL* 1.3 78.7 - - - +
114O PHE* 1.3 70.5 + - - +
215O GLU* 3.3 44.5 + - - -
216O PHE 4.6 0.4 - - - -
217O ILE* 4.7 9.0 - - - -
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Residues in contact with PHE 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61M HIS* 4.2 32.3 - + + -
112O VAL* 3.7 2.5 - - - +
113O CYS* 1.3 91.4 - - - +
115O ASP* 1.3 60.9 + - - +
116O HIS* 4.3 28.5 - + - -
212O VAL* 4.2 16.6 - - + -
213O CYS* 3.5 12.1 - - - -
214O ALA* 3.0 28.4 - - - +
215O GLU* 2.8 40.6 + - + +
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Residues in contact with ASP 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLU* 4.2 4.7 - - - +
112O VAL* 3.7 16.6 - - + +
114O PHE* 1.3 74.5 - - - +
116O HIS* 1.3 74.7 + - - +
117O CYS 3.2 0.7 + - - -
118O THR* 3.0 39.3 + - - -
121O ARG* 3.1 46.4 - - + -
122O PRO* 3.4 6.6 - - - +
213O CYS 4.0 0.9 - - - -
214O ALA* 3.7 8.4 - - + +
216O PHE* 4.1 5.7 - - - -
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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