Contacts of the strand formed by residues 249 - 253 (chain A) in PDB entry 4QY2
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 ARG 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LEU 5.3 1.2 - - - +
70A LEU* 4.6 12.9 - - - +
71A THR* 4.3 10.3 - - - +
110A LYS* 3.1 36.6 + - + +
111A ILE 3.4 7.6 - - - +
112A SER* 4.0 17.4 - - - +
113A THR* 4.0 1.8 - - - -
140A ALA* 5.1 2.2 - - - +
141A GLU* 2.9 58.4 + - + +
142A LEU* 5.6 0.5 - - - +
172A MET 5.3 2.3 + - - +
247A PRO* 4.1 8.5 - - - +
248A SER* 1.3 88.3 - - - +
250A VAL* 1.3 71.2 + - - +
251A SER* 5.5 0.2 + - - -
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Residues in contact with VAL 250 (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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110A LYS* 3.4 11.1 - - - +
111A ILE* 2.8 45.3 + - + +
113A THR* 3.6 21.5 - - + -
161A TYR* 3.5 34.8 - - + +
169A HIS* 4.0 11.4 - - + +
170A LEU 3.6 10.8 - - - +
171A ILE* 3.7 34.1 - - + +
172A MET 5.6 0.2 - - - +
247A PRO* 5.0 0.2 - - + -
249A ARG* 1.3 74.1 - - - +
251A SER* 1.3 64.6 + - - +
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Residues in contact with SER 251 (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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60A LEU* 3.5 31.1 + - - +
108A ILE* 4.5 2.9 - - - -
109A ASN 3.4 5.4 - - - -
110A LYS* 3.2 24.6 - - - -
111A ILE* 5.4 0.9 - - - -
169A HIS* 3.6 7.5 - - - +
170A LEU* 2.8 46.0 + - - +
172A MET* 6.1 0.3 - - - +
250A VAL* 1.3 76.9 - - - +
252A LYS* 1.3 63.9 + - - +
253A LEU* 4.3 2.2 - - - -
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Residues in contact with LYS 252 (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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108A ILE* 3.3 4.7 - - - -
109A ASN* 2.8 51.6 + - + +
111A ILE* 5.1 5.8 - - + -
165A ASP* 2.9 25.5 + - - +
166A THR* 5.8 0.4 + - - -
167A ALA* 4.1 20.0 - - + +
168A GLU 3.9 10.5 - - - +
169A HIS* 3.9 24.5 - - + +
170A LEU 4.9 0.9 - - - +
251A SER* 1.3 76.0 - - - +
253A LEU* 1.3 69.8 + - - +
254A ILE* 3.2 28.9 - - + +
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Residues in contact with LEU 253 (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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60A LEU* 4.5 13.9 - - + -
101A LYS* 3.9 44.0 - - + +
102A ILE* 4.0 11.0 - - + +
105A SER* 4.1 12.1 - - - +
107A GLY 3.6 2.5 - - - +
108A ILE* 3.9 26.5 - - + -
168A GLU 5.3 1.0 + - - -
170A LEU* 4.5 20.3 - - + +
251A SER* 4.8 5.6 - - - -
252A LYS* 1.3 83.5 - - - +
254A ILE* 1.3 62.0 + - - +
255A GLY 4.0 2.9 + - - +
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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