Contacts of the helix formed by residues 87 - 104 (chain K) 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 ASP 87 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27J GLU* 3.5 29.4 - - - +
59J PRO* 4.9 1.0 - - - +
62J ILE* 5.3 2.3 - - - +
84K LEU* 3.3 10.7 + - + +
85K LEU 3.3 0.2 - - - -
86K ASP* 1.3 81.2 - - - +
88K PRO* 1.3 74.1 - - - +
89K PRO* 3.0 22.5 - - - +
90K ALA* 2.9 27.1 + - + +
91K LEU 3.0 8.8 + - - -
124N GLU* 5.1 10.5 - - - +
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Residues in contact with PRO 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K LEU 4.4 0.2 - - - -
85K LEU 4.4 5.8 - - - +
86K ASP* 4.1 2.2 - - - +
87K ASP* 1.3 86.3 - - - +
89K PRO* 1.3 63.5 - - + +
91K LEU* 3.6 10.8 - - + +
92K ASP* 2.6 39.2 + - - +
122N ALA* 4.3 31.2 - - + +
124N GLU* 5.4 9.9 - - + +
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Residues in contact with PRO 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J PRO* 3.8 22.5 - - + +
87K ASP* 3.0 22.2 - - - +
88K PRO* 1.3 101.6 - - + +
90K ALA* 1.3 60.1 + - - +
92K ASP* 3.3 7.5 - - + +
93K ALA* 3.0 22.9 + - - +
124N GLU* 4.3 19.3 - - + +
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Residues in contact with ALA 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59J PRO* 3.7 19.2 - - + +
62J ILE* 4.1 20.2 - - + -
63J ALA* 4.2 1.9 - - - +
84K LEU* 3.9 15.9 - - + +
87K ASP* 2.9 31.2 + - + +
89K PRO* 1.3 73.1 - - - +
91K LEU* 1.3 68.8 - - - +
93K ALA* 3.0 4.5 + - - +
94K ALA* 2.7 23.6 + - - +
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Residues in contact with LEU 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81K ALA* 3.3 32.8 - - + +
84K LEU* 3.2 26.1 - - + +
85K LEU* 3.6 36.6 - - + +
87K ASP 3.0 6.5 + - - +
88K PRO* 3.6 11.2 - - + +
90K ALA* 1.3 75.4 - - - +
92K ASP* 1.3 64.3 + - - +
94K ALA* 3.1 3.9 + - + +
95K LEU* 2.8 51.1 + - + +
143K ILE* 5.4 2.5 - - + -
146K LYS* 5.9 5.2 - - - +
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Residues in contact with ASP 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88K PRO 2.6 21.9 + - - +
89K PRO* 3.3 9.0 - - + +
91K LEU* 1.3 76.0 - - - +
93K ALA* 1.3 66.4 + - - +
95K LEU* 2.9 6.8 + - - +
96K ASP* 2.8 26.8 + - - +
146K LYS* 3.9 28.5 + - - +
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Residues in contact with ALA 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59J PRO* 4.7 1.1 - - + -
60J ALA* 4.3 26.2 - - + +
63J ALA* 4.4 5.4 - - + -
67J ARG* 5.4 0.9 - - - -
89K PRO 3.0 9.4 + - - +
90K ALA* 3.0 8.9 + - - +
92K ASP* 1.3 80.1 + - - +
94K ALA* 1.3 63.7 + - - +
96K ASP* 3.1 8.0 + - - +
97K HIS* 3.0 24.6 + - - +
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Residues in contact with ALA 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63J ALA* 4.0 13.6 - - + +
67J ARG* 4.6 4.5 + - - +
80K LEU* 4.2 20.9 - - + +
81K ALA* 6.0 0.9 - - - -
84K LEU* 3.7 22.0 - - + -
90K ALA 2.7 16.3 + - - +
91K LEU* 3.4 12.1 - - + +
93K ALA* 1.3 72.8 - - - +
95K LEU* 1.3 61.9 + - + +
97K HIS* 3.5 8.8 + - - +
98K LEU* 3.4 21.9 + - - +
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Residues in contact with LEU 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81K ALA* 4.2 9.0 - - + -
91K LEU* 2.8 46.4 + - + +
92K ASP 3.5 2.5 - - - +
94K ALA* 1.3 75.6 - - + +
96K ASP* 1.3 57.7 + - - +
97K HIS 3.0 2.0 - - - -
98K LEU* 2.7 33.4 + - + +
99K ALA* 2.8 11.8 + - - +
143K ILE* 3.6 27.4 - - + -
146K LYS* 4.2 40.4 - - + +
147K ILE* 3.4 30.9 - - + -
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Residues in contact with ASP 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92K ASP* 2.8 20.5 + - - +
93K ALA* 3.5 12.8 - - - +
95K LEU* 1.3 71.9 - - - +
97K HIS* 1.3 63.7 + - - +
99K ALA* 2.8 25.5 + - - +
100K HIS* 3.1 29.2 + - - -
146K LYS* 5.0 5.9 + - + +
149K SER* 5.6 1.6 + - - -
150K ARG* 4.2 16.6 + - - -
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Residues in contact with HIS 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J ARG* 3.8 32.1 + - - -
67J ARG* 3.6 38.8 + - - +
160J HEM 3.3 36.3 + - - -
93K ALA 3.0 11.7 + - - +
94K ALA 3.5 11.4 + - - +
96K ASP* 1.3 78.8 + - - +
98K LEU* 1.3 63.6 + - - +
100K HIS* 3.2 15.8 + + + +
101K GLN* 3.1 47.3 + - + +
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Residues in contact with LEU 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67J ARG* 6.1 2.9 - - - -
77K GLY* 4.9 12.3 - - - +
80K LEU* 5.5 9.0 - - + -
81K ALA* 5.5 1.1 - - + -
94K ALA 3.6 12.1 - - - +
95K LEU* 2.7 29.3 + - + +
97K HIS* 1.3 75.7 - - - +
99K ALA* 1.3 61.9 + - - +
101K GLN* 3.3 23.2 + - - +
102K HIS* 2.9 32.2 + - + +
147K ILE* 3.9 34.3 - - + -
160K HEM 4.1 38.8 - - + -
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Residues in contact with ALA 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K LEU 2.8 4.6 + - - -
96K ASP* 2.8 17.6 + - - +
98K LEU* 1.3 77.4 - - - +
100K HIS* 1.3 52.1 + - - +
102K HIS* 2.8 7.6 + - - +
103K GLU* 2.8 32.2 + - - +
146K LYS 3.8 14.4 - - - +
147K ILE 3.0 23.2 + - - +
149K SER* 4.4 3.1 - - - +
150K ARG* 3.7 28.5 - - + +
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Residues in contact with HIS 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96K ASP* 3.1 39.2 + - - -
97K HIS* 3.2 12.5 + + + +
99K ALA* 1.3 79.9 - - - +
101K GLN* 1.3 61.7 + - + +
102K HIS 3.1 0.7 + - - -
103K GLU* 3.3 29.0 + - - +
104K VAL* 3.6 19.2 + - - +
150K ARG* 3.1 38.7 + - - +
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Residues in contact with GLN 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95J GLN* 4.8 1.6 + - - -
160J HEM 3.3 29.5 + - - +
97K HIS* 3.1 33.2 + - + +
98K LEU* 3.4 29.3 - - - +
99K ALA 3.2 0.6 - - - -
100K HIS* 1.3 76.1 - - + +
102K HIS* 1.3 63.6 + - + +
104K VAL* 4.2 6.6 - - - +
105K ARG* 3.2 22.2 - - - +
160K HEM 3.6 41.7 + - + +
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Residues in contact with HIS 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98K LEU* 2.9 23.2 + - + +
99K ALA 2.8 7.9 + - - +
101K GLN* 1.3 83.6 - - + +
103K GLU* 1.3 65.7 + - - +
104K VAL 3.3 2.2 - - - -
105K ARG* 3.1 24.3 + - - +
108K VAL* 4.5 5.1 - - + +
113K PHE* 3.7 17.7 - + + -
147K ILE* 4.3 13.4 - - + +
148K SER* 5.9 0.2 - - - -
150K ARG 5.5 0.2 - - - +
151K LEU* 3.9 17.8 - - + +
160K HEM 2.0 97.3 + + + -
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Residues in contact with GLU 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K ALA 2.8 13.8 + - - +
100K HIS* 3.3 25.5 + - - +
102K HIS* 1.3 78.6 - - - +
104K VAL* 1.3 65.6 + - + +
105K ARG 3.1 8.3 + - - -
106K GLU* 4.4 2.4 + - - -
150K ARG* 3.3 55.1 + - + +
151K LEU* 4.6 5.2 - - - +
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Residues in contact with VAL 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100K HIS 3.6 15.9 + - - +
101K GLN* 4.2 11.2 - - - +
103K GLU* 1.3 83.7 - - + +
105K ARG* 1.3 67.6 + - - +
106K GLU 3.6 4.7 + - - -
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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