Contacts of the helix formed by residues 135 - 144 (chain C) in PDB entry 3DV1
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 PRO 135 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C SER* 3.6 23.8 - - - +
38C PHE 6.1 0.2 - - - +
120C GLY 4.6 3.8 - - - +
121C LEU 5.9 0.2 - - - -
122C ALA 3.9 11.2 - - - +
123C TYR 4.0 3.4 - - - -
124C ALA* 3.5 37.5 - - + +
127C ALA* 4.7 0.4 - - + -
133C LEU 3.4 6.5 - - - +
134C GLU* 1.3 89.4 - - + +
136C PHE* 1.3 66.0 + - - +
137C PHE* 4.7 3.1 - - + +
138C ASP* 3.1 32.5 + - - +
139C SER* 3.2 18.1 + - - -
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Residues in contact with PHE 136 (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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18C MET* 3.8 17.3 - - + -
36C SER 4.9 0.8 + - - -
38C PHE* 4.3 24.8 - + + +
85C VAL* 3.8 20.6 - - + -
87C ILE* 4.2 19.1 - - + -
95C VAL* 3.7 28.9 - - + -
97C ALA* 3.7 20.2 - - + -
98C ASN 5.8 1.9 + - - +
119C LEU* 3.5 36.6 - - + -
120C GLY 4.8 4.5 + - - +
121C LEU* 5.2 0.4 - - + -
134C GLU 3.9 0.6 + - - -
135C PRO* 1.3 72.0 - - - +
137C PHE* 1.3 73.9 + + + +
139C SER* 3.0 10.2 + - - -
140C LEU* 2.9 41.0 + - + +
176C ILE* 6.1 0.4 - - + -
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Residues in contact with PHE 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C GLY 5.3 1.4 + - - -
121C LEU* 4.2 29.5 - - + +
135C PRO* 3.4 2.7 - - + +
136C PHE* 1.3 85.8 - + - +
138C ASP* 1.3 63.1 + - - +
140C LEU* 3.2 24.0 + - + +
141C VAL* 2.9 49.6 + - + +
147C PRO 4.2 5.2 - - - -
149C LEU 3.6 36.6 - - - -
150C PHE* 3.9 15.9 - + + -
176C ILE* 4.0 17.9 - - + -
347C ARG* 3.3 41.5 - - - +
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Residues in contact with ASP 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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122C ALA 4.6 2.4 - - - +
123C TYR* 4.9 5.2 - - - -
124C ALA* 4.5 5.6 + - - -
134C GLU* 3.8 16.6 - - + +
135C PRO* 3.1 39.8 + - - +
137C PHE* 1.3 77.6 - - - +
139C SER* 1.3 57.5 + - - +
141C VAL* 3.4 5.4 + - - +
142C LYS* 2.9 30.7 + - - +
347C ARG* 3.1 25.3 + - - +
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Residues in contact with SER 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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95C VAL* 4.9 2.2 - - - -
96C ARG 4.1 9.1 + - - -
97C ALA* 4.5 13.9 - - - +
98C ASN* 5.0 1.2 + - - -
134C GLU* 2.4 40.5 + - - +
135C PRO 3.2 5.4 + - - -
136C PHE 3.0 9.7 + - - -
138C ASP* 1.3 79.2 - - - +
140C LEU* 1.3 56.9 + - - +
142C LYS* 3.3 2.2 + - - +
143C GLN* 2.9 52.2 + - - +
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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
----------------------------------------------------------
87C ILE* 5.4 2.5 - - + -
91C PRO* 4.9 2.7 - - + -
93C VAL* 3.8 23.3 - - + -
95C VAL* 3.8 28.2 - - + +
136C PHE* 2.9 31.6 + - + +
137C PHE* 3.4 26.5 - - + +
139C SER* 1.3 76.7 - - - +
141C VAL* 1.3 55.0 + - - +
144C THR* 2.7 46.5 + - - +
146C VAL* 4.3 10.5 - - + -
176C ILE* 3.8 31.4 - - + -
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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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137C PHE* 2.9 49.1 + - + +
138C ASP* 3.8 5.8 - - - +
140C LEU* 1.3 78.1 - - + +
142C LYS* 1.3 58.8 + - - +
144C THR 3.0 18.2 - - - +
146C VAL* 4.0 21.1 - - + +
147C PRO 4.2 0.7 - - - +
148C ASN* 3.7 33.4 - - + +
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Residues in contact with LYS 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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134C GLU* 4.4 17.4 + - - +
138C ASP 2.9 17.5 + - - +
139C SER* 3.9 5.2 - - - +
141C VAL* 1.3 80.4 - - - +
143C GLN* 1.3 65.1 + - + +
144C THR 4.4 1.4 - - - +
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Residues in contact with GLN 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 THR 4.5 1.5 - - - +
95C VAL* 3.3 17.2 - - + -
96C ARG* 2.8 51.4 + - - +
134C GLU* 4.6 3.6 + - - -
139C SER* 2.9 29.3 + - - +
142C LYS* 1.3 82.5 - - + +
144C THR* 1.3 62.6 + - + +
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Residues in contact with THR 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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93C VAL* 3.8 33.2 - - + -
94C THR 4.8 2.9 - - - +
95C VAL* 3.6 23.6 - - + -
140C LEU* 2.7 23.1 + - + +
141C VAL 3.0 18.2 - - - +
142C LYS 4.4 1.6 - - - +
143C GLN* 1.3 84.1 - - + +
145C HIS* 1.3 70.9 + - - +
146C VAL* 3.1 22.4 + - - +
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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