Contacts of the strand formed by residues 254 - 260 (chain A) in PDB entry 3H44
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 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A GLY 4.4 0.9 - - - +
73A ILE* 3.4 19.3 - - + -
74A LYS* 3.2 24.6 + - - +
90A LEU* 3.8 27.4 - - + -
91A ASP 3.3 2.2 - - - -
92A VAL* 4.0 8.5 - - + -
169A PHE* 4.0 18.8 - - + +
249A TYR* 3.6 53.4 - - + +
250A SER 3.8 8.5 - - - +
251A SER* 3.6 19.5 - - - +
252A ASN 3.3 3.7 + - - +
253A LEU* 1.3 81.9 - - - +
255A ALA* 1.3 61.2 + - - +
278A VAL* 4.1 13.7 - - + -
442A HIS* 3.8 5.4 - - - -
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Residues in contact with ALA 255 (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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74A LYS* 3.3 10.1 - - + +
89A ALA 3.8 0.3 - - - +
90A LEU* 3.2 7.4 - - - +
91A ASP 2.8 32.0 + - - +
254A MET* 1.3 75.1 - - - +
256A VAL* 1.3 62.6 + - - +
438A ALA* 3.3 28.1 - - - +
441A LEU* 3.6 22.9 - - + -
442A HIS* 3.6 12.8 - - + +
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Residues in contact with VAL 256 (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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73A ILE* 3.5 23.3 - - + -
74A LYS 2.9 9.4 + - - +
75A VAL* 3.1 14.5 - - + +
76A LEU 2.9 24.8 + - - +
88A ALA* 5.3 1.1 - - + -
89A ALA 3.3 11.9 - - - +
90A LEU* 3.8 20.2 - - + -
165A PHE* 5.7 0.9 - - + -
255A ALA* 1.3 76.5 - - - +
257A VAL* 1.3 68.1 + - - +
258A VAL* 3.9 22.9 - - + -
271A VAL* 5.0 4.0 - - + -
275A PHE* 4.4 30.7 - - + -
441A LEU* 3.8 0.7 - - - +
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Residues in contact with VAL 257 (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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76A LEU* 3.2 17.7 - - + +
78A ILE* 3.8 29.2 - - + -
88A ALA* 3.1 6.1 - - - -
89A ALA 3.0 30.5 + - - +
256A VAL* 1.3 77.4 - - - +
258A VAL* 1.3 67.6 + - - +
259A LEU 4.3 0.2 - - - -
434A THR* 3.6 25.9 - - + +
437A ILE* 3.9 13.9 - - + -
438A ALA* 3.4 33.0 - - - +
441A LEU* 4.1 6.1 - - + -
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Residues in contact with VAL 258 (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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75A VAL* 5.5 0.2 - - - +
76A LEU 3.0 8.3 + - - -
77A LEU* 3.5 14.8 - - + +
78A ILE 2.7 33.4 + - - +
87A SER 3.6 6.3 - - - +
88A ALA* 3.7 13.7 - - + -
158A LEU* 4.0 30.5 - - + -
162A LEU* 4.3 13.0 - - + -
256A VAL* 3.9 11.4 - - + -
257A VAL* 1.3 80.8 - - - +
259A LEU* 1.3 58.1 + - - +
267A LEU* 4.0 15.0 - - + +
270A LEU* 4.8 2.5 - - + -
271A VAL* 3.9 20.6 - - + -
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Residues in contact with LEU 259 (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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62A ARG* 4.8 10.5 - - - +
78A ILE* 3.1 43.1 - - + +
80A ASP* 4.7 6.1 - - + +
83A THR* 4.0 24.9 - - + +
85A LYS 4.0 4.3 - - - +
86A SER* 3.2 5.5 - - - -
87A SER 2.9 36.9 + - - +
158A LEU* 4.3 2.9 - - - +
257A VAL 4.3 0.2 - - - -
258A VAL* 1.3 78.4 - - - +
260A GLY* 1.3 61.2 + - - +
430A PRO* 3.8 31.2 - - + -
433A TYR* 4.3 13.2 - - + -
434A THR* 4.0 12.1 - - + +
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Residues in contact with GLY 260 (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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78A ILE 3.1 5.5 + - - -
79A SER* 3.5 5.7 - - - -
80A ASP 2.9 20.3 + - - -
83A THR* 4.0 10.5 - - - -
86A SER* 3.1 16.2 - - - -
158A LEU* 4.9 1.1 - - - -
258A VAL 4.4 0.2 + - - -
259A LEU* 1.3 75.3 - - - +
261A ARG* 1.3 64.9 + - - -
262A GLU* 3.1 11.9 + - - +
267A LEU* 4.4 6.3 - - - +
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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