Contacts of the strand formed by residues 153 - 157 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E ILE* 3.5 31.0 - - + +
81F PRO 3.8 18.2 - - - -
82F SER 4.4 1.1 - - - -
84F PHE* 3.8 20.0 - + - -
151F PRO* 3.4 19.4 - - - +
152F ASP* 1.3 84.0 - - + +
154F LYS* 1.3 63.6 + - - +
169F VAL* 3.9 19.5 - - + -
170F ILE 3.1 8.3 - - - -
171F PHE* 3.3 43.7 - + + -
172F ASN* 4.1 0.4 - - - +
217F SER* 3.6 27.6 - - - -
219F LEU* 3.8 25.1 - - + -
220F LEU* 3.9 13.2 - - + -
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Residues in contact with LYS 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F ASP* 4.9 12.1 + - - -
151F PRO* 4.3 13.7 - - + -
153F PHE* 1.3 75.8 - - - +
155F THR* 1.3 61.3 + - - +
156F ILE* 4.3 14.5 - - + +
168F LYS 3.5 2.1 - - - +
169F VAL* 3.2 5.1 - - - -
170F ILE* 2.8 47.7 + - + +
172F ASN* 3.9 28.3 - - + +
214G ASN 3.0 28.3 + - - +
215G LYS* 4.2 6.9 - - - +
216G ALA 3.5 20.0 + - - -
218G SER* 5.3 4.4 - - - +
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Residues in contact with THR 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E ILE* 3.9 19.9 - - - +
103F PRO* 4.4 17.0 - - + -
104F ARG 5.0 5.5 - - - +
105F ASN* 4.3 4.3 - - - +
153F PHE 4.2 0.2 + - - -
154F LYS* 1.3 72.5 + - - +
156F ILE* 1.3 64.2 + - - +
157F LEU 4.3 0.5 + - - -
167F TRP* 4.9 4.0 - - + -
168F LYS 3.8 2.7 - - - +
169F VAL* 4.2 14.0 - - + +
224F PHE* 5.2 2.4 - - + -
228F PHE* 4.2 25.1 - - + -
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Residues in contact with ILE 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F ASN* 3.5 11.2 - - - +
154F LYS* 4.3 16.8 - - + -
155F THR* 1.3 79.2 - - - +
157F LEU* 1.3 65.2 + - - +
158F GLU 3.5 0.5 + - - -
167F TRP* 3.2 10.4 - - - +
168F LYS* 2.9 62.6 + - + +
170F ILE* 3.7 29.8 - - + -
213G PRO 6.0 0.2 - - - +
214G ASN* 4.4 5.4 - - - +
218G SER* 4.2 21.1 - - - -
221G SER* 6.0 2.0 - - - +
222G SER* 3.2 30.7 - - - +
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Residues in contact with LEU 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F TYR* 3.7 27.4 - - + -
103F PRO 3.8 4.7 - - - +
104F ARG* 3.8 31.5 - - + -
105F ASN* 2.9 30.5 + - - +
155F THR 4.3 0.2 + - - -
156F ILE* 1.3 72.1 - - - +
158F GLU* 1.3 70.4 + - - +
160F PRO* 4.7 1.8 - - + -
165F VAL* 3.9 15.9 - - + -
166F GLY 3.8 8.3 - - - +
167F TRP* 3.6 32.7 - - + +
60G THR* 4.2 6.1 - - + -
222G SER* 3.1 7.4 - - - +
225G SER* 3.8 16.4 - - - +
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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