Contacts of the strand formed by residues 153 - 157 (chain C) in PDB entry 3M4D
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 PHE 153 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ILE* 3.4 30.8 - - + +
81C PRO 3.8 20.4 - - - -
82C SER 4.4 1.6 - - - -
84C PHE* 4.0 20.4 - + - -
151C PRO* 3.2 20.8 - - - +
152C ASP* 1.3 84.3 - - + +
154C LYS* 1.3 63.3 + - - +
155C THR 4.3 0.3 + - - -
169C VAL* 3.8 19.7 - - + -
170C ILE 3.2 23.1 - - - -
171C PHE* 3.3 29.2 - + + -
172C ASN 4.1 0.4 - - - +
217C SER* 3.7 27.1 - - - -
219C LEU* 3.7 20.2 - - + -
220C LEU* 4.0 14.6 - - + -
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Residues in contact with LYS 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ASP* 4.7 13.3 + - - +
148C TYR* 5.4 4.7 + - - -
151C PRO* 4.3 13.2 - - + -
153C PHE* 1.3 76.1 - - - +
155C THR* 1.3 61.1 + - - +
156C ILE* 3.9 15.0 - - + -
168C LYS 3.5 2.1 - - - +
169C VAL* 3.1 5.5 - - - -
170C ILE* 2.9 50.0 + - + +
172C ASN* 3.6 27.4 - - - +
214D ASN 3.0 27.7 + - - +
215D LYS* 4.3 3.4 - - - +
216D ALA 3.5 22.0 + - - +
218D SER* 4.8 7.7 + - - +
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Residues in contact with THR 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ILE* 3.9 20.3 - - - +
103C PRO* 4.3 15.5 - - + -
104C ARG 4.9 5.9 - - - +
105C ASN* 4.3 4.7 - - - +
153C PHE 4.3 0.4 + - - -
154C LYS* 1.3 73.1 - - - +
156C ILE* 1.3 63.6 + - - +
157C LEU 4.3 0.3 + - - -
167C TRP* 4.8 4.7 - - + -
168C LYS 3.8 2.2 - - - -
169C VAL* 4.0 14.3 - - + +
224C PHE* 5.2 2.4 - - + -
228C PHE* 4.2 26.5 - - + -
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Residues in contact with ILE 156 (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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105C ASN* 3.5 11.4 - - - +
154C LYS* 4.3 15.9 - - + -
155C THR* 1.3 79.4 - - - +
157C LEU* 1.3 66.4 + - - +
158C GLU 3.5 0.5 + - - -
167C TRP* 3.1 10.4 - - - +
168C LYS* 2.8 63.9 + - + +
170C ILE* 4.0 24.5 - - + -
214D ASN* 4.4 9.9 - - - +
218D SER* 3.6 25.1 - - - +
222D SER* 3.3 29.4 - - - +
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Residues in contact with LEU 157 (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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101C TYR* 3.6 31.9 - - + -
103C PRO 3.8 11.2 - - - +
104C ARG* 3.8 18.7 - - - -
105C ASN* 2.9 34.3 + - - +
155C THR 4.3 0.4 + - - -
156C ILE* 1.3 72.1 - - - +
158C GLU* 1.3 70.7 + - - +
160C PRO* 4.6 6.7 - - + -
165C VAL* 4.0 15.7 - - + -
166C GLY 3.6 13.5 - - - +
167C TRP* 3.6 30.0 - - + +
60D THR* 5.1 1.6 - - - +
222D SER* 3.2 8.0 - - - +
225D SER* 3.8 15.5 - - - +
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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