Contacts of the helix formed by residues 129 - 140 (chain C) in PDB entry 4LQL
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 GLY 129 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C MET* 3.7 14.6 - - - +
82C THR 3.3 23.6 - - - -
83C PHE* 4.3 8.3 - - - -
84C SER 4.4 5.4 - - - +
125C GLN 3.8 0.2 + - - -
126C SER 2.6 10.0 + - - -
128C HIS* 1.3 75.8 - - - +
130C ASP* 1.3 68.7 + - - +
132C GLU* 3.6 5.4 + - - +
133C TYR* 3.1 19.1 + - - +
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Residues in contact with ASP 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B MET* 5.1 6.5 - - + -
79C TRP* 5.9 2.7 - - + +
80C MET* 4.7 6.6 + - - +
102C HIS* 5.3 4.3 - - + -
104C ALA* 3.8 29.4 - - + -
105C THR 5.8 0.2 - - - +
126C SER* 2.8 15.5 + - - +
127C ALA* 4.7 6.5 - - - +
129C GLY* 1.3 77.4 - - - +
131C ARG* 1.3 57.9 + - + +
133C TYR* 2.7 30.0 + - - +
134C ALA* 2.9 13.1 + - - +
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Residues in contact with ARG 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ASP* 2.9 30.1 + - - +
344B ILE* 4.7 8.7 - - - +
432B LEU* 5.6 1.4 - - - +
436B ALA* 3.5 34.7 + - - +
439B TRP* 3.8 28.4 - - + +
440B MET* 4.9 7.4 - - + +
443B GLY 5.4 0.5 - - - -
444B GLY 4.5 5.1 + - - +
445B GLY* 3.7 43.5 + - - -
446B HIS* 4.2 8.7 - - - +
127C ALA* 3.0 27.1 + - - +
128C HIS* 4.1 7.5 - - - +
130C ASP* 1.3 81.8 - - + +
132C GLU* 1.3 59.3 + - - +
134C ALA* 3.9 8.5 + - - +
135C TYR* 3.4 16.6 + - - +
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Residues in contact with GLU 132 (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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188B VAL* 3.0 28.2 - - - +
189B ALA 3.1 13.5 + - - -
190B VAL* 2.9 36.5 - - - +
446B HIS* 3.8 8.4 + - + +
83C PHE* 4.6 7.4 - - + -
84C SER 3.8 14.1 - - - +
85C PRO* 4.0 0.3 - - - +
86C ALA* 2.9 47.4 + - + +
128C HIS 3.8 15.3 + - - +
129C GLY* 3.6 5.0 + - - +
130C ASP 2.9 1.0 + - - -
131C ARG* 1.3 79.2 - - - +
133C TYR* 1.3 64.4 + - - +
135C TYR* 3.7 9.2 + - - +
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Residues in contact with TYR 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C THR* 5.7 8.1 - - - -
80C MET* 4.0 22.0 - - + -
84C SER 5.3 0.8 + - - -
86C ALA* 4.5 5.4 - - - -
89C TRP* 4.7 18.4 - + - -
100C LEU* 6.6 0.2 - - + -
102C HIS* 4.6 17.3 - + + -
129C GLY 3.1 13.4 + - - +
130C ASP* 2.7 17.4 + - - +
132C GLU* 1.3 71.0 - - - +
134C ALA* 1.3 62.7 + - - +
136C ILE* 3.0 23.9 + - + +
137C ASN* 3.2 14.8 + - + +
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Residues in contact with ALA 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B MET* 3.4 44.4 - - + +
443B GLY* 4.6 3.1 - - - -
102C HIS* 5.4 7.4 - - + -
130C ASP 2.9 12.3 + - - +
131C ARG* 4.0 6.3 - - - +
133C TYR* 1.3 75.2 - - - +
135C TYR* 1.3 68.2 + - - +
137C ASN* 3.8 8.1 - - - +
138C SER* 2.9 22.7 + - - -
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Residues in contact with TYR 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ALA* 4.9 3.6 - - + -
190B VAL* 3.4 44.0 - - + -
394B SER* 6.2 2.9 - - - -
395B TYR 5.8 2.5 - - - -
396B PHE* 6.4 2.0 - + - -
443B GLY* 4.6 12.7 - - - -
444B GLY 4.9 5.2 - - - +
86C ALA* 5.6 1.1 - - + -
131C ARG 3.4 8.4 + - - +
132C GLU 3.8 6.7 - - - +
133C TYR 3.1 0.8 + - - -
134C ALA* 1.3 79.2 - - - +
136C ILE* 1.3 65.2 + - + +
138C SER* 2.9 1.2 + - - -
139C ARG* 2.6 47.4 + - + +
196D VAL* 5.7 1.3 - - + -
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Residues in contact with ILE 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ALA* 4.4 8.7 - - + -
86C ALA* 3.8 17.0 - - + +
89C TRP* 4.0 26.7 - - + +
90C ILE* 3.6 39.9 - - + -
93C THR* 4.4 10.2 - - - +
132C GLU 4.0 0.2 + - - -
133C TYR* 3.0 15.6 + - + +
135C TYR* 1.3 81.2 - - + +
137C ASN* 1.3 61.6 + - + +
139C ARG* 3.7 13.7 - - + -
140C LEU* 3.0 42.7 + - + +
196D VAL* 4.0 20.9 - - + -
200D ILE* 4.7 2.0 - - + -
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Residues in contact with ASN 137 (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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93C THR* 5.1 5.2 - - - +
100C LEU* 4.8 14.8 - - + -
102C HIS* 6.5 0.9 - - + -
133C TYR* 3.2 18.6 + - + +
134C ALA* 3.8 6.3 - - - +
135C TYR 3.2 1.2 - - - -
136C ILE* 1.3 77.7 - - + +
138C SER* 1.3 59.4 + - - +
140C LEU 4.2 0.9 - - - -
142C VAL* 3.2 46.9 + - + +
144C ALA* 5.8 3.8 - - + -
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Residues in contact with SER 138 (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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396B PHE* 6.6 0.4 - - - -
440B MET 4.4 1.3 + - - -
441B LYS 3.0 28.3 - - - -
442B TYR 4.4 1.3 - - - -
443B GLY* 4.1 13.5 - - - -
134C ALA 2.9 16.5 + - - -
135C TYR 2.9 3.1 + - - -
137C ASN* 1.3 74.2 - - - +
139C ARG* 1.3 65.4 - - - +
140C LEU 3.1 1.8 - - - -
141C ASN* 2.9 19.3 + - - +
142C VAL 5.8 0.2 - - - -
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Residues in contact with ARG 139 (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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192B GLU 5.4 1.2 + - - -
395B TYR* 3.4 21.6 + - - -
396B PHE* 4.2 23.2 - - + +
397B ASP* 3.6 37.5 - - - +
135C TYR* 2.6 31.1 + - + +
136C ILE* 3.7 17.3 - - + +
138C SER* 1.3 72.9 - - - +
140C LEU* 1.3 56.8 + - - +
141C ASN* 3.4 9.9 + - - -
194D ASP* 2.9 27.1 + - - -
196D VAL* 4.0 18.7 - - - +
197D ALA* 3.6 16.8 - - - +
200D ILE* 3.6 28.6 - - + +
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Residues in contact with LEU 140 (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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90C ILE* 5.5 2.2 - - + +
93C THR* 4.7 12.6 - - - -
94C GLU* 5.3 11.7 - - + +
136C ILE* 3.0 39.1 + - + +
138C SER 3.1 0.2 - - - -
139C ARG* 1.3 77.0 - - + +
141C ASN* 1.3 59.3 + - - +
142C VAL* 2.8 29.1 + - + +
200D ILE* 4.3 27.1 - - + -
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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