Contacts of the helix formed by residues 79 - 93 (chain D) in PDB entry 2GTP
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 ASN 79 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D LEU* 5.3 2.6 - - - +
65D GLU* 3.2 27.4 - - - +
69D TRP* 3.7 20.2 - - - +
75D LYS 4.3 3.0 + - - +
76D LEU 3.8 5.2 + - - +
78D ALA* 1.3 80.0 - - + +
80D GLN* 1.3 65.7 + - - +
81D THR* 4.5 6.5 - - - +
82D GLY 3.5 15.5 - - - +
83D GLN* 3.1 27.7 + - - +
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Residues in contact with GLN 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ASN* 1.3 71.6 - - - +
81D THR* 1.3 70.6 + - - +
83D GLN* 3.5 20.0 - - - +
84D ASN* 3.1 36.2 + - - +
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Residues in contact with THR 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D LEU* 3.2 46.7 - - + +
69D TRP* 3.9 7.9 - - + -
79D ASN* 3.3 6.0 - - - +
80D GLN* 1.3 83.1 - - - +
82D GLY* 1.3 62.8 + - - +
84D ASN* 3.1 13.4 + - - +
85D VAL* 3.0 27.7 + - + +
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Residues in contact with GLY 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D TRP* 3.4 26.9 - - - -
76D LEU* 3.5 24.7 - - - +
79D ASN* 3.3 8.5 + - - +
81D THR* 1.3 78.7 - - - +
83D GLN* 1.3 56.3 + - - +
85D VAL* 3.3 0.7 + - - +
86D PHE* 2.9 33.7 + - - +
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Residues in contact with GLN 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D LEU 3.8 0.8 + - - -
77D LEU* 2.9 46.9 + - + +
78D ALA 4.0 4.4 + - - -
79D ASN 3.1 20.5 + - - +
80D GLN* 3.5 19.4 - - - +
82D GLY* 1.3 76.0 - - - +
84D ASN* 1.3 53.7 + - - +
86D PHE 3.8 0.2 - - - -
87D GLY* 2.7 33.4 + - - -
99D ILE* 3.8 11.4 - - + +
102D TRP* 4.6 5.8 - - + -
103D LEU* 3.3 33.2 - - + +
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Residues in contact with ASN 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D GLN* 3.1 26.3 + - - +
81D THR* 3.1 12.0 + - - +
83D GLN* 1.3 81.0 - - - +
85D VAL* 1.3 58.7 + - + +
87D GLY* 3.3 2.1 + - - -
88D SER* 2.9 31.9 + - - -
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D TRP* 4.4 9.6 - - + -
81D THR* 3.0 23.4 + - + +
82D GLY 3.3 3.5 + - - +
84D ASN* 1.3 76.2 - - + +
86D PHE* 1.3 65.3 + - - +
88D SER* 3.4 9.4 + - - -
89D PHE* 3.2 16.5 + - - +
177D PHE* 3.8 23.3 - - + -
182D ILE* 3.8 20.6 - - + +
183D TYR* 5.2 2.9 - - - +
186D LEU* 4.2 32.8 - - + -
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Residues in contact with PHE 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D LEU* 4.0 19.1 - - + -
76D LEU* 3.9 19.1 - - + -
77D LEU* 3.9 9.9 - - + -
82D GLY 2.9 17.1 + - - +
83D GLN* 4.0 2.5 - - - +
85D VAL* 1.3 75.0 - - - +
87D GLY* 1.3 64.8 + - - +
89D PHE* 3.1 3.7 + + - +
90D LEU* 2.9 59.1 + - + +
99D ILE* 3.7 20.4 - - + -
169D MET* 3.9 21.3 - - + -
173D SER* 4.3 9.9 - - - -
174D TYR* 4.2 14.4 - - + -
177D PHE* 3.7 39.5 - + + -
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Residues in contact with GLY 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D GLN 2.7 19.2 + - - -
84D ASN* 3.6 2.5 - - - -
86D PHE* 1.3 75.1 - - - +
88D SER* 1.3 55.9 + - - +
90D LEU* 3.1 5.5 + - - +
91D LYS* 2.9 28.0 + - - +
96D GLU* 4.4 3.5 - - - +
99D ILE* 4.3 21.3 - - - +
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Residues in contact with SER 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ASN 2.9 16.1 + - - -
85D VAL* 3.4 11.4 - - - -
87D GLY* 1.3 74.2 - - - +
89D PHE* 1.3 61.3 + - - +
91D LYS* 3.2 9.5 + - - +
92D SER* 3.2 20.8 + - - -
182D ILE* 4.5 14.7 - - - +
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Residues in contact with PHE 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D VAL 3.2 5.0 + - - +
86D PHE* 3.1 10.1 + + - +
88D SER* 1.3 79.3 - - - +
90D LEU* 1.3 73.9 + - + +
92D SER* 2.6 28.7 + - - -
93D GLU* 3.1 42.6 + - + +
173D SER 3.5 11.7 - - - -
176D ARG* 3.8 8.7 - - + -
177D PHE* 3.4 54.1 - + + -
180D SER* 3.4 31.2 - - - -
182D ILE* 3.9 17.4 - - + +
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Residues in contact with LEU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D PHE* 2.9 47.6 + - + +
87D GLY* 3.5 6.5 - - - +
89D PHE* 1.3 82.6 - - + +
91D LYS* 1.3 57.6 + - - +
93D GLU* 3.1 4.1 + - - +
94D PHE 2.9 23.2 + - - -
95D SER* 2.9 38.1 + - - +
96D GLU* 3.6 15.0 - - + +
98D ASN* 4.8 0.2 - - + -
99D ILE* 3.8 25.6 - - + +
169D MET* 4.1 10.8 - - + -
173D SER* 3.7 26.5 - - - +
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Residues in contact with LYS 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D GLY 2.9 12.4 + - - +
88D SER* 3.5 13.0 - - - +
89D PHE 3.2 0.4 - - - -
90D LEU* 1.3 77.6 - - - +
92D SER* 1.3 60.6 + - - +
94D PHE* 3.1 21.1 + - - -
96D GLU* 4.0 29.0 - - + +
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Residues in contact with SER 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ILE 4.4 2.3 - - - +
88D SER 3.2 8.9 + - - -
89D PHE* 2.6 34.7 + - - -
91D LYS* 1.3 75.8 - - - +
93D GLU* 1.3 62.5 + - - +
94D PHE* 3.8 14.7 - - - -
182D ILE* 4.2 9.4 - - - +
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Residues in contact with GLU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A THR 4.9 1.3 - - - +
183A GLY* 3.0 4.0 - - - -
184A ILE 2.7 40.3 + - - +
185A VAL* 3.6 15.4 - - + +
89D PHE* 3.1 43.2 + - + +
90D LEU* 3.1 7.8 + - - +
92D SER* 1.3 83.3 - - - +
94D PHE* 1.3 65.6 + - - +
95D SER* 3.3 10.4 + - - +
173D SER* 4.5 6.6 + - - -
176D ARG* 3.0 43.7 + - - +
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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