Contacts of the helix formed by residues 102 - 110 (chain D) in PDB entry 4GCK
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 102 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D GLU* 5.6 0.2 - - - -
65D PHE* 4.8 5.5 - - - -
98D PHE* 2.9 49.5 + - + +
99D GLY 3.2 3.4 - - - -
101D ARG* 1.3 96.4 - - - +
103D PRO* 1.3 67.1 - - - +
104D GLY 3.2 2.5 - - - -
105D LEU* 3.0 33.6 + - + +
106D THR* 2.9 20.6 + - - -
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Residues in contact with PRO 103 (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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24D GLU* 3.7 31.0 - - + +
99D GLY 3.5 6.0 - - - +
100D GLU 3.7 12.3 - - - +
101D ARG 3.6 7.6 - - - +
102D ASN* 1.3 88.1 - - - +
104D GLY* 1.3 63.0 + - - +
106D THR* 3.0 13.7 + - - +
107D ARG* 3.2 9.9 + - - +
173D PHE* 4.1 10.3 - - + -
178D PHE* 3.6 47.6 - - + -
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Residues in contact with GLY 104 (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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20D ALA* 3.9 6.1 - - - -
23D LEU* 3.5 23.9 - - - +
24D GLU* 3.4 31.5 + - - +
102D ASN 3.2 1.0 - - - -
103D PRO* 1.3 80.0 - - - +
105D LEU* 1.3 64.1 + - - +
107D ARG* 3.3 17.5 - - - +
108D ILE* 3.7 2.8 + - - +
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Residues in contact with LEU 105 (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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20D ALA* 4.4 16.4 - - + -
23D LEU* 5.5 0.2 - - + -
62D LEU* 3.7 33.9 - - + +
65D PHE* 3.6 36.1 - - + -
66D ILE* 4.0 21.2 - - + +
98D PHE* 4.1 7.0 - - + -
102D ASN* 3.0 31.6 + - + +
104D GLY* 1.3 75.0 - - - +
106D THR* 1.3 61.5 + - - +
108D ILE* 2.9 31.8 + - + +
109D LEU* 2.9 14.0 + - - +
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Residues in contact with THR 106 (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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98D PHE* 6.2 0.2 - - - -
99D GLY* 2.8 38.6 + - - -
102D ASN 2.9 6.5 + - - -
103D PRO* 3.0 11.2 + - - -
105D LEU* 1.3 76.5 - - - +
107D ARG* 1.3 53.2 + - - +
109D LEU* 2.9 10.1 + - - +
110D THR* 2.7 43.6 + - + -
170D LEU* 4.1 20.4 - - + -
173D PHE* 4.0 14.8 - - + -
174D VAL* 3.8 20.2 - - + -
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Residues in contact with ARG 107 (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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115C MET* 6.3 0.4 - - - -
23D LEU* 2.6 39.0 + - + +
25D SER 2.9 20.8 + - - -
26D SER* 4.9 4.0 - - - +
28D GLY* 3.5 20.3 + - - -
29D SER* 3.6 26.5 - - - +
103D PRO 3.2 6.7 + - - +
104D GLY 3.3 12.1 - - - +
105D LEU 3.1 0.2 - - - -
106D THR* 1.3 75.5 - - - +
108D ILE* 1.3 60.2 + - - +
110D THR* 3.5 6.9 + - - -
112D HIS* 3.3 18.1 + - + -
113D ALA* 2.9 33.9 + - + -
174D VAL* 4.4 25.1 + - + +
177D GLU* 5.1 10.9 - - - +
178D PHE* 3.3 34.3 - - + -
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Residues in contact with ILE 108 (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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23D LEU* 3.9 11.2 - - + -
59D PHE* 3.9 13.7 - - + +
62D LEU* 3.9 39.0 - - + -
63D ILE* 3.8 25.8 - - + -
66D ILE* 4.2 5.6 - - + -
104D GLY 4.1 3.6 - - - +
105D LEU* 2.9 22.6 + - + +
107D ARG* 1.3 79.3 - - - +
109D LEU* 1.3 60.5 + - - +
110D THR 3.2 0.2 - - - -
111D GLY* 2.9 20.4 + - - -
113D ALA* 4.1 16.6 - - + -
114D LEU* 3.7 25.6 - - + +
125D ILE* 4.1 9.2 - - + +
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Residues in contact with LEU 109 (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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175C ARG* 5.3 1.2 - - - -
66D ILE* 4.3 20.4 - - + -
70D LEU* 4.8 10.3 - - + -
95D ILE* 5.5 5.2 - - + +
98D PHE* 4.9 11.2 - - + -
99D GLY* 5.3 2.9 - - - -
105D LEU 2.9 11.0 + - - +
106D THR* 3.3 19.5 - - + +
108D ILE* 1.3 79.6 - - - +
110D THR* 1.3 59.6 + - - +
111D GLY 3.5 0.2 + - - -
122D GLN* 5.3 0.5 - - - +
125D ILE* 3.6 15.4 - - + +
128D LEU* 4.2 24.9 - - + -
129D PHE* 3.5 52.0 - - + -
132D ILE* 6.2 0.4 - - + -
170D LEU* 4.1 23.8 - - + -
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Residues in contact with THR 110 (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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112C HIS* 2.8 23.9 + - - -
171C SER* 6.0 1.7 - - - -
175C ARG* 5.7 6.2 - - - +
106D THR* 2.7 24.6 + - + +
107D ARG* 3.5 5.9 + - - -
109D LEU* 1.3 72.8 - - + +
111D GLY* 1.3 56.5 + - - +
112D HIS* 2.6 30.7 + - - -
122D GLN* 4.9 1.1 - - - -
167D GLU 5.3 0.4 - - - +
170D LEU* 3.8 33.0 - - + +
171D SER* 4.0 5.6 - - - +
174D VAL* 3.6 23.4 - - + +
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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