Contacts of the strand formed by residues 112 - 116 (chain A) in PDB entry 6YBX
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 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ILE 3.9 7.6 - - - +
51A TRP* 4.6 0.7 - - - -
52A ALA 5.2 0.2 - - - +
86A THR* 3.8 39.7 - - + +
87A LEU 3.9 6.1 - - - -
88A ALA* 3.6 36.3 - - + +
102A ILE* 3.9 16.3 - - + +
110A VAL 4.2 0.7 - - - +
111A PRO* 1.3 76.8 - - - +
113A ASN* 1.3 73.8 + - - +
114A PHE* 4.9 0.2 - - + -
125A ARG* 3.4 5.5 - - - +
126A CYS 2.9 33.9 + - - +
201A VAL* 4.1 9.2 - - + -
202A THR 3.4 6.7 - - - +
203A PHE* 3.8 27.1 - - + -
205A PRO* 3.8 5.9 - - - +
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Residues in contact with ASN 113 (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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112A MET* 1.3 76.9 - - - +
114A PHE* 1.3 61.0 + - - +
115A SER* 2.7 34.4 + - - +
123A GLY 5.6 0.3 - - - -
124A VAL 3.5 6.5 + - - +
125A ARG* 2.8 37.8 + - - +
200A ARG 4.6 1.8 + - - -
201A VAL* 3.4 3.8 - - - -
202A THR* 2.9 42.9 + - - +
205A PRO* 3.7 21.5 - - + +
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Residues in contact with PHE 114 (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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3A PHE* 3.8 9.4 - + - -
88A ALA* 3.6 17.5 - - + -
89A GLU 3.4 28.9 - - - -
90A PHE* 3.9 19.1 - + - -
100A ILE* 3.6 33.0 - - + +
101A ASP 3.5 19.1 - - - -
102A ILE* 4.0 15.7 - - + +
112A MET* 4.9 0.7 - - + -
113A ASN* 1.3 73.6 - - - +
115A SER* 1.3 63.1 + - - +
123A GLY* 3.3 2.3 - - - -
124A VAL* 2.9 34.1 + - + +
199A TYR* 3.8 29.8 - + + -
200A ARG 3.6 3.4 - - - -
201A VAL* 3.8 16.2 - - + +
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Residues in contact with SER 115 (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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100A ILE* 5.1 0.2 - - - -
113A ASN* 2.7 29.6 + - - +
114A PHE* 1.3 74.0 + - - +
116A PRO* 1.3 77.1 - - - +
123A GLY* 3.6 11.3 - - - -
199A TYR* 3.3 7.8 - - - +
200A ARG* 2.8 38.4 + - - +
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Residues in contact with PRO 116 (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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100A ILE* 4.7 4.9 - - + -
114A PHE 4.6 0.4 - - - +
115A SER* 1.3 95.1 - - - +
117A THR* 1.3 61.8 - - - +
118A THR* 3.5 18.6 - - - +
119A ARG* 4.9 2.4 + - - -
121A CYS* 3.4 43.7 - - - +
122A ARG 3.5 21.3 - - - +
123A GLY* 3.8 0.9 - - - +
197A SER* 5.1 1.3 - - - -
198A ASN 3.3 11.9 - - - +
199A TYR* 3.7 10.4 - - + -
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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