Contacts of the strand formed by residues 62 - 66 (chain L) in PDB entry 1H2I
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 LYS 62 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A LEU* 4.1 10.3 - - + -
183A PRO 4.8 4.9 - - - +
184A LEU* 4.7 6.6 - - - +
185A GLU* 3.8 34.6 + - + +
54L SER* 3.5 31.9 - - - -
55L ARG 3.7 0.2 - - - -
56L MET* 3.4 25.5 - - + +
61L GLN* 1.3 79.1 - - - +
63L VAL* 1.3 66.1 + - - +
64L CYS* 4.3 16.2 - - - -
176L ASN* 3.8 28.0 + - - +
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Residues in contact with VAL 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L SER* 3.0 5.6 - - - -
55L ARG* 3.0 63.7 + - + +
57L ALA* 3.5 30.1 - - + +
61L GLN* 3.5 2.7 - - + +
62L LYS* 1.3 79.9 - - - +
64L CYS* 1.3 73.5 + - - +
65L TYR* 3.8 3.1 - - + -
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Residues in contact with CYS 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L ILE* 3.9 16.6 - - + -
53L SER 3.3 3.8 - - - -
54L SER* 4.3 11.7 - - - -
62L LYS* 4.3 20.2 + - - -
63L VAL* 1.3 83.2 - - - +
65L TYR* 1.3 64.3 + - - +
166L ILE* 3.4 23.3 - - + +
172L LEU* 3.9 28.0 - - + +
175L LEU* 5.7 1.8 - - - -
176L ASN* 6.0 2.2 - - - -
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Residues in contact with TYR 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L ILE* 3.9 2.5 - - - -
53L SER* 2.9 54.7 + - - +
54L SER* 3.8 28.4 + - - -
55L ARG* 3.3 39.6 - - + +
63L VAL* 3.8 10.1 - - + -
64L CYS* 1.3 76.6 - - - +
66L ILE* 1.3 76.5 + - - +
67L GLU* 3.7 24.2 + - + -
152L LYS* 4.2 13.7 - - - +
156L ARG* 6.2 2.9 - - - +
166L ILE* 3.6 10.0 - - - +
169M LYS* 5.4 4.7 + - - -
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Residues in contact with ILE 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L LEU* 4.3 16.8 - - + -
51L TYR* 3.9 20.9 - - + +
52L ILE* 4.2 12.8 - - + -
65L TYR* 1.3 80.9 - - - +
67L GLU* 1.3 68.7 + - - +
70L ARG* 3.9 13.7 - - + -
71L VAL* 3.7 26.2 - - + +
74L LEU* 5.0 2.2 - - + -
152L LYS* 2.7 30.3 + - + +
156L ARG* 4.9 8.9 - - - +
162L LEU 5.0 0.9 - - - +
163L GLY* 3.8 28.0 - - - +
165L CYS* 5.9 0.2 - - - -
166L ILE* 3.9 21.5 - - + +
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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