Contacts of the strand formed by residues 125 - 129 (chain A) in PDB entry 5L0U
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 MET 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLN* 3.6 0.3 - - - -
91A ILE* 2.8 46.7 + - + +
122A LEU* 4.2 10.1 - - + -
123A PRO* 3.3 30.1 - - + +
124A ASP* 1.3 77.1 - - - +
126A GLU* 1.3 63.0 + - - +
127A MET* 4.0 13.7 - - - +
363A LEU* 3.3 54.3 - - + +
366A TYR* 4.1 12.1 - - + -
367A SER* 3.6 19.7 - - - -
370A LEU* 4.2 7.2 - - + -
374A VAL* 3.6 16.5 - - - +
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Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A MET* 3.5 18.4 - - + +
88A HIS* 2.7 26.9 + - - +
89A TYR 3.3 15.3 - - - +
90A GLN* 3.0 24.3 + - + -
125A MET* 1.3 76.2 - - - +
127A MET* 1.3 68.1 + - - +
366A TYR* 2.8 22.5 + - - -
370A LEU* 3.7 7.7 - - + +
372A TYR* 2.7 40.7 + - - +
374A VAL* 4.0 14.4 - - + +
375A THR 5.1 0.9 + - - -
377A ARG* 5.3 0.2 + - - -
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Residues in contact with MET 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A MET* 4.5 4.3 - - - -
87A THR 3.8 0.3 - - - +
88A HIS* 3.5 4.2 - - - -
89A TYR* 2.9 50.7 + - + +
91A ILE* 3.9 26.9 - - + -
96A LEU* 4.8 0.7 - - + -
115A ILE* 4.2 10.8 - - + -
125A MET* 4.0 15.3 - - - +
126A GLU* 1.3 86.2 - - - +
128A VAL* 1.3 63.4 + - - +
129A ILE* 3.9 25.7 + - + -
148A PHE* 3.6 20.4 - - + -
363A LEU* 4.2 18.6 - - + -
366A TYR* 3.6 16.2 - - + +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A MET* 4.3 7.0 - - - -
80A VAL* 3.6 33.0 - - + +
81A VAL* 3.7 30.3 - - + +
85A LEU* 4.0 3.8 - - - +
86A GLY* 3.3 42.0 - - - +
87A THR 3.5 2.7 - - - -
88A HIS* 4.4 5.8 - - + -
127A MET* 1.3 77.1 - - - +
129A ILE* 1.3 59.0 + - - +
130A ASN 3.9 0.2 + - - -
146A PRO 4.5 6.7 + - - +
147A VAL* 3.7 6.7 - - + -
148A PHE* 3.0 28.3 + - - -
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Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A THR* 2.8 40.5 + - - +
89A TYR* 3.7 24.2 - - + -
111A VAL* 3.9 16.8 - - + -
115A ILE* 3.8 24.9 - - + -
127A MET* 3.9 23.6 - - + -
128A VAL* 1.3 73.5 - - - +
130A ASN* 1.3 60.6 + - - +
131A VAL* 3.5 9.2 + - + +
148A PHE* 3.7 12.3 - - + -
161A TYR* 3.6 36.8 - - + +
359A TRP* 4.3 9.2 - - + -
363A LEU* 5.6 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