Contacts of the helix formed by residues 102 - 110 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C PHE* 4.5 6.3 - - - -
98C PHE* 2.9 49.0 + - + +
99C GLY* 3.1 3.8 - - - -
101C ARG* 1.3 96.9 - - - +
103C PRO* 1.3 66.4 - - - +
104C GLY 3.3 1.8 - - - -
105C LEU* 3.1 34.2 + - + +
106C THR* 2.9 21.8 + - - -
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Residues in contact with PRO 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLU* 3.1 39.7 - - + +
99C GLY 3.3 6.9 - - - +
100C GLU 3.7 13.0 - - - +
101C ARG 3.4 7.6 - - - +
102C ASN* 1.3 89.0 - - - +
104C GLY* 1.3 64.6 + - - +
106C THR* 3.1 13.1 + - - +
107C ARG 3.1 9.2 + - - -
173C PHE* 4.1 8.3 - - + -
178C PHE* 3.5 37.5 - - + -
181C ARG* 5.7 3.6 - - - +
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Residues in contact with GLY 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ALA* 3.4 24.0 + - - -
23C LEU* 3.4 28.8 - - - +
24C GLU* 3.6 11.5 - - - +
102C ASN 3.3 1.0 - - - -
103C PRO* 1.3 79.7 - - - +
105C LEU* 1.3 61.3 + - - +
107C ARG* 3.2 19.1 + - - +
108C ILE 3.7 2.6 + - - -
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ALA* 4.1 19.7 - - + +
62C LEU* 3.6 37.7 - - + -
65C PHE* 3.7 31.6 - - + -
66C ILE* 3.8 17.8 - - + +
98C PHE* 3.8 14.1 - - + -
102C ASN* 3.1 32.3 + - + +
104C GLY* 1.3 72.4 - - - +
106C THR* 1.3 59.9 + - - +
107C ARG 3.1 0.2 - - - -
108C ILE* 3.0 14.4 + - + +
109C LEU* 2.9 26.7 + - - +
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Residues in contact with THR 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C PHE* 5.7 1.0 - - - -
99C GLY* 2.9 40.2 + - - -
102C ASN 2.9 6.5 + - - -
103C PRO* 3.1 11.0 + - - -
105C LEU* 1.3 75.7 - - - +
107C ARG* 1.3 54.0 + - - +
109C LEU* 3.0 10.5 + - + +
110C THR* 2.7 34.3 + - + -
170C LEU* 3.8 34.3 - - + -
173C PHE* 4.1 9.9 - - + -
174C VAL* 3.7 19.7 - - + -
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Residues in contact with ARG 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LEU* 2.6 31.9 + - + +
25C SER 3.3 15.8 + - - -
28C GLY* 3.1 32.3 + - - -
29C SER* 3.8 6.9 - - - +
103C PRO 3.1 10.3 + - - +
104C GLY 3.3 13.2 - - - +
105C LEU 3.1 0.2 - - - -
106C THR* 1.3 76.9 - - - +
108C ILE* 1.3 56.2 + - - +
110C THR* 3.4 6.5 + - - -
112C HIS* 3.3 27.5 + - + -
113C ALA* 2.9 38.4 + - + +
174C VAL* 4.1 23.1 + - + +
177C GLU* 3.1 39.4 + - - -
178C PHE* 3.4 16.0 - - + -
115D MET* 4.8 4.1 - - - +
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Residues in contact with ILE 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LEU* 3.7 25.4 - - + -
59C PHE* 4.1 15.7 - - + +
62C LEU* 3.9 29.2 - - + -
63C ILE* 4.0 19.3 - - + -
66C ILE* 4.0 14.6 - - + -
104C GLY 4.2 0.4 - - - +
105C LEU* 3.0 18.1 + - + +
107C ARG* 1.3 77.3 - - - +
109C LEU* 1.3 59.8 + - - +
111C GLY* 2.9 21.5 + - - -
113C ALA* 3.8 20.6 - - + -
114C LEU* 3.8 20.6 - - + +
125C ILE* 4.1 9.7 - - + +
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Residues in contact with LEU 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ILE* 4.1 18.4 - - + -
70C LEU* 4.7 10.5 - - + -
95C ILE* 5.3 7.4 - - + +
98C PHE* 5.1 9.9 - - + -
99C GLY* 5.8 1.1 - - - -
105C LEU 2.9 12.9 + - - +
106C THR* 3.5 15.3 - - + +
108C ILE* 1.3 79.2 - - - +
110C THR* 1.3 59.9 + - - +
111C GLY 3.4 0.3 + - - -
125C ILE* 3.7 17.0 - - + +
128C LEU* 4.1 26.2 - - + -
129C PHE* 3.3 52.0 - - + -
132C ILE* 6.1 0.4 - - + -
170C LEU* 4.0 24.0 - - + -
175D ARG* 5.3 1.7 - - - -
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Residues in contact with THR 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C THR 2.7 24.2 + - - +
107C ARG 3.4 6.4 + - - -
108C ILE 3.2 0.2 - - - -
109C LEU* 1.3 71.8 - - - +
111C GLY* 1.3 56.1 + - - +
112C HIS* 2.7 30.1 + - - -
122C GLN* 5.6 0.2 - - - -
129C PHE* 5.6 0.9 - - + -
167C GLU* 5.1 1.3 - - - +
170C LEU* 3.8 33.2 - - + +
171C SER* 3.9 10.5 - - - +
174C VAL* 3.5 22.0 - - + +
112D HIS* 2.9 23.6 + - - -
171D SER* 4.8 8.4 + - - +
175D ARG* 5.5 7.6 - - - +
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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