Contacts of the helix formed by residues 136 - 146 (chain C) in PDB entry 3EU9
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 HIS 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A SO4 3.6 25.5 + - - -
98C ALA 3.6 11.2 - - - -
99C ILE 2.9 28.2 + - - -
100C ASN* 4.0 1.8 - - - -
101C ASN* 3.6 34.2 + - + +
131C ALA* 3.1 10.1 + - + +
134C GLN* 3.4 27.0 - - + +
135C GLY* 1.3 76.8 + - - +
137C LEU* 1.3 64.5 + - - +
138C SER 3.3 0.9 - - - -
139C MET* 3.1 16.5 + - + +
140C VAL* 3.0 23.9 + - - +
172C ILE* 3.9 3.1 - - - +
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Residues in contact with LEU 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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170A THR* 4.2 20.0 - - + +
171A SER* 4.5 0.7 - - - -
174A ALA* 3.8 23.8 - - + -
209A LEU* 4.2 11.2 - - + -
135C GLY 3.3 7.2 + - - +
136C HIS* 1.3 72.2 - - - +
138C SER* 1.3 63.6 + - - +
140C VAL* 3.2 3.8 + - + +
141C VAL* 3.0 33.7 + - + +
171C SER* 3.8 32.1 - - - +
172C ILE* 4.0 17.9 - - + +
175C TYR* 4.3 23.8 - - + -
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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
----------------------------------------------------------
205A ASP* 4.2 2.4 + - - -
208A ARG* 4.0 18.7 + - - -
209A LEU* 3.5 40.5 + - - +
212A THR* 3.5 21.2 + - - +
101C ASN* 4.3 7.4 - - - -
103C ILE* 3.8 10.3 - - - -
136C HIS 3.3 0.6 - - - -
137C LEU* 1.3 78.5 - - - +
139C MET* 1.3 58.3 + - - +
141C VAL* 3.4 2.4 + - - +
142C GLN* 3.0 27.7 + - - +
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Residues in contact with MET 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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97C ALA 3.6 6.1 - - - +
98C ALA* 3.4 17.7 - - - +
101C ASN* 3.4 18.3 - - - +
102C ARG 3.4 37.0 - - - +
103C ILE* 3.6 13.7 - - + +
106C VAL* 3.5 35.2 - - + -
131C ALA* 3.5 14.8 - - + -
136C HIS* 3.1 15.1 + - + +
138C SER* 1.3 76.9 - - - +
140C VAL* 1.3 67.2 + - - +
142C GLN* 4.2 3.8 - - - -
143C LEU* 2.9 36.1 + - + +
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Residues in contact with VAL 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C LEU* 3.7 15.9 - - + +
131C ALA* 4.6 1.6 - - + -
132C THR* 3.8 27.8 - - - +
136C HIS 3.0 18.7 + - - +
137C LEU* 3.5 9.9 - - + +
139C MET* 1.3 75.4 - - - +
141C VAL* 1.3 63.4 + - - +
143C LEU 3.6 0.2 + - - -
144C MET* 3.0 46.6 + - - +
172C ILE* 4.0 26.2 - - + -
175C TYR* 4.3 12.3 - - + -
176C LEU* 4.3 11.0 - - + -
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Residues in contact with VAL 141 (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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209A LEU* 4.3 7.4 - - + -
212A THR* 4.2 14.8 - - + +
213A PHE* 3.7 39.9 - - + -
137C LEU* 3.0 26.2 + - + +
138C SER 3.5 7.9 - - - +
140C VAL* 1.3 77.1 - - - +
142C GLN* 1.3 56.7 + - - +
144C MET* 3.4 2.3 + - - +
145C LYS* 2.9 38.0 + - + +
175C TYR* 3.7 34.4 + - + +
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Residues in contact with GLN 142 (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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212A THR* 4.1 19.8 + - + +
103C ILE* 3.0 28.1 - - + +
106C VAL* 4.0 22.0 - - + -
107C LYS* 2.9 48.9 - - - +
138C SER 3.0 17.5 + - - +
139C MET* 3.3 6.5 + - - +
141C VAL* 1.3 76.7 - - - +
143C LEU* 1.3 64.0 + - - +
145C LYS* 3.1 15.2 + - - +
146C TYR* 3.1 35.0 - - + -
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Residues in contact with LEU 143 (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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94C LEU* 4.6 17.0 - - + -
98C ALA* 4.0 4.5 - - + -
106C VAL* 3.7 27.8 - - + -
110C ILE* 4.6 5.2 - - + -
116C VAL* 4.4 7.9 - - + +
127C PRO* 3.9 9.4 - - + +
128C LEU* 3.6 40.4 - - + +
131C ALA* 4.3 0.4 - - + -
139C MET* 2.9 39.6 + - + +
142C GLN* 1.3 76.0 - - - +
144C MET* 1.3 64.0 + - - +
146C TYR* 2.9 16.8 + - - +
147C GLY 3.3 0.3 + - - -
148C ALA* 3.0 29.3 + - + +
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Residues in contact with MET 144 (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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128C LEU* 4.0 12.8 - - + -
140C VAL* 3.0 40.5 + - - +
141C VAL* 3.9 4.0 - - - +
143C LEU* 1.3 76.6 - - - +
145C LYS* 1.3 61.9 + - - +
147C GLY* 2.9 14.2 + - - -
148C ALA 3.9 17.6 - - - +
150C PRO* 3.9 23.1 - - + -
175C TYR* 4.1 12.3 - - + +
176C LEU* 3.8 17.3 - - + -
179C LYS* 3.9 35.2 - - + +
181C GLN* 6.0 0.4 - - + -
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Residues in contact with LYS 145 (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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212A THR 5.3 3.8 - - - +
213A PHE* 4.2 26.8 - - - +
214A ASN* 5.6 4.3 - - - +
141C VAL* 2.9 24.3 + - + +
142C GLN* 3.1 21.3 + - - +
144C MET* 1.3 77.3 - - - +
146C TYR* 1.3 62.7 + - + +
147C GLY 3.4 2.6 + - - -
175C TYR* 3.9 19.0 + - - -
179C LYS* 4.9 9.5 - - - +
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Residues in contact with TYR 146 (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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107C LYS* 3.2 38.6 + - + +
110C ILE* 3.6 47.3 - - + -
111C SER* 5.8 0.4 - - - -
116C VAL* 3.8 17.1 - - + +
142C GLN* 3.1 49.1 + - + -
143C LEU 2.9 11.0 + - - +
145C LYS* 1.3 81.6 - - + +
147C GLY* 1.3 58.6 + - - -
148C ALA 3.5 0.4 + - - -
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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