Contacts of the helix formed by residues 103 - 111 (chain C) in PDB entry 6GL7
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 LEU 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C LYS 3.0 0.8 - - - -
102C GLU* 1.3 83.2 - - + +
104C GLN* 1.3 76.9 + - - +
105C CYS 3.2 0.2 - - - -
106C LEU* 3.0 8.6 + - - +
107C GLN* 2.9 34.6 + - + +
261C ASP* 5.5 4.7 - - - +
262C HIS* 3.9 32.8 - - + +
263C LEU* 4.8 11.4 - - + +
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Residues in contact with GLN 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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41C VAL* 3.9 14.4 - - + -
101C LYS* 3.2 40.2 + - + +
103C LEU* 1.3 89.9 + - + +
105C CYS* 1.3 63.5 + - - +
106C LEU 3.0 0.2 - - - -
107C GLN* 4.3 15.0 - - - +
108C ILE* 3.0 41.4 + - + +
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Residues in contact with CYS 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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40C CYS* 2.9 36.5 - - + +
41C VAL* 3.6 16.9 - - + +
95C CYS* 2.1 51.1 - - + -
99C MET* 4.0 11.4 - - - -
101C LYS 3.1 11.6 + - - +
102C GLU 2.9 29.4 - - - -
103C LEU 3.2 0.4 - - - -
104C GLN* 1.3 77.2 - - - +
106C LEU* 1.3 61.7 + - - +
109C TYR* 3.7 6.5 + - - +
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Residues in contact with LEU 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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40C CYS* 5.9 0.2 - - - -
95C CYS* 4.1 8.3 - - + -
102C GLU 3.7 14.8 - - - +
103C LEU* 3.0 6.5 + - - +
105C CYS* 1.3 81.7 - - - +
107C GLN* 1.3 59.9 + - - +
108C ILE 3.2 1.3 - - - -
109C TYR* 3.1 2.4 + - - -
110C TRP* 2.8 41.9 + - + +
127C PRO* 4.2 12.6 - - + -
128C TYR* 3.6 49.6 - - + +
262C HIS* 3.4 27.6 - - + +
263C LEU* 4.0 6.7 - - - -
266C SER* 3.3 24.5 - - - +
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Residues in contact with GLN 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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103C LEU* 2.9 29.6 + - + +
104C GLN* 4.2 14.1 - - - +
106C LEU* 1.3 72.4 - - - +
108C ILE* 1.3 64.6 + - + +
110C TRP* 3.9 1.0 - - - +
111C SER* 3.0 27.1 + - - -
262C HIS* 3.7 36.2 + - + +
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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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40C CYS 4.1 3.1 - - - +
41C VAL* 3.9 34.5 - - + +
44C ASN* 3.5 38.4 - - + +
57C TYR* 5.0 9.0 - - + +
90C LEU* 3.6 19.4 - - + +
104C GLN* 3.0 30.0 + - + +
105C CYS 5.0 0.7 - - - +
107C GLN* 1.3 76.8 - - + +
109C TYR* 1.3 64.8 + - - +
111C SER* 2.6 25.9 + - - +
112C ILE 4.0 0.2 + - - -
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Residues in contact with TYR 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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40C CYS* 4.2 0.7 - - - -
90C LEU* 3.7 15.7 - - + +
91C TYR* 4.8 4.5 - + - -
92C ASP* 3.9 26.7 + - - -
93C CYS* 3.3 33.2 - - - -
94C ARG* 4.5 7.2 + - - -
105C CYS 3.7 15.8 + - - +
106C LEU* 3.1 8.2 + - - +
108C ILE* 1.3 79.5 - - - +
110C TRP* 1.3 71.5 + + - +
112C ILE* 3.0 28.0 - - + +
113C HIS* 3.2 37.7 + + - -
125C ALA* 5.2 5.9 - - + +
127C PRO* 3.5 38.8 - - + +
114F ARG* 4.6 11.1 + - - -
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Residues in contact with TRP 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 LEU* 2.8 37.5 + - + +
109C TYR* 1.3 77.5 - + - +
111C SER* 1.3 62.1 + - - +
112C ILE 3.1 0.2 - - - -
113C HIS* 3.1 62.1 + + + +
124C GLU* 5.0 3.6 - - + -
125C ALA* 3.9 32.3 - - + -
127C PRO* 3.6 29.9 - - + +
262C HIS* 3.5 23.6 - - + -
265C ARG* 3.4 47.4 - - - +
266C SER* 3.6 16.6 + - - -
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Residues in contact with SER 111 (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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57C TYR* 3.1 36.0 + - - +
60C LEU* 4.0 18.4 - - - +
61C ARG* 4.8 14.0 + - - +
107C GLN* 3.0 19.1 + - - -
108C ILE 2.6 19.9 + - - -
109C TYR 3.1 0.2 - - - -
110C TRP* 1.3 76.8 - - - +
112C ILE* 1.3 56.1 + - - +
113C HIS 3.4 4.5 + - - +
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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