Contacts of the strand formed by residues 82 - 89 (chain A) in PDB entry 1P1C
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 ILE 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ALA* 3.0 47.8 - - + +
60A GLY* 3.3 15.3 - - - -
61A GLY 4.3 0.2 - - - +
63A VAL* 3.3 23.6 - - + -
77A VAL* 4.2 13.9 - - + +
78A GLN* 5.2 1.1 - - - +
80A ALA* 2.5 18.8 + - + +
81A PRO* 1.3 80.6 - - - +
83A LYS* 1.3 62.0 + - - +
84A GLU 3.5 26.5 - - - +
85A HIS* 4.6 5.8 - - + +
107A HIS* 3.0 35.9 + - + +
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Residues in contact with LYS 83 (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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61A GLY* 2.8 31.4 + - - +
62A ARG* 3.6 37.1 - - - +
81A PRO 5.2 0.7 - - - +
82A ILE* 1.3 75.4 - - - +
84A GLU* 1.3 92.7 + - + +
107A HIS* 4.0 5.5 - - - +
108A LYS* 3.9 15.8 + - - +
129A ASP* 4.2 1.2 + - - -
160A LYS* 4.1 14.8 - - - +
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Residues in contact with GLU 84 (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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61A GLY 2.9 5.5 + - - +
62A ARG* 2.9 36.2 + - + -
63A VAL* 3.0 23.7 + - - +
82A ILE* 3.5 10.0 - - - +
83A LYS* 1.3 99.7 - - + +
85A HIS* 1.3 61.2 + - - +
86A TRP* 2.9 30.2 + - - +
108A LYS* 3.2 36.2 + - + +
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Residues in contact with HIS 85 (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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63A VAL* 3.6 15.0 - - + +
65A GLU* 3.1 32.0 + - + +
74A ALA* 3.5 26.0 - - + -
77A VAL* 3.6 24.9 - - + +
78A GLN* 2.8 38.0 + - - +
82A ILE* 4.9 2.7 - - + -
84A GLU* 1.3 74.4 - - - +
86A TRP* 1.3 69.0 + - - +
87A ILE* 4.0 7.4 + - + +
101A TRP* 3.7 13.4 - + - -
108A LYS 2.6 10.6 + - - +
109A VAL* 2.7 31.7 - - + +
110A VAL 2.8 2.6 + - - -
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Residues in contact with TRP 86 (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* 3.3 26.5 - - + +
63A VAL 2.9 6.7 + - - +
64A LEU* 3.2 9.3 - - + +
65A GLU* 2.7 25.6 + - - +
84A GLU* 2.9 26.7 + - - -
85A HIS* 1.3 83.0 - - - +
87A ILE* 1.3 61.0 + - - +
108A LYS* 5.0 3.8 - - - -
110A VAL* 3.1 47.7 - - + +
112A LEU* 4.0 15.7 - - + -
123A LEU* 4.0 19.3 - - + -
124A PRO* 5.7 1.6 - - + -
127A HIS* 3.8 24.9 - + - -
128A PHE* 3.8 27.1 - + + -
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Residues in contact with ILE 87 (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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65A GLU* 2.9 23.1 - - + +
67A GLY 3.5 4.3 - - - +
68A PHE* 3.3 36.1 - - + +
74A ALA* 6.0 0.2 - - + -
85A HIS* 4.1 27.6 - - + +
86A TRP* 1.3 77.9 - - - +
88A ILE* 1.3 87.4 + - - +
98A LEU* 3.1 37.3 - - + +
101A TRP* 4.8 2.5 - - + -
109A VAL* 4.6 7.6 - - + -
110A VAL 3.3 6.0 + - - +
111A PRO* 3.7 3.2 - - + +
112A LEU* 3.1 24.3 + - - +
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Residues in contact with ILE 88 (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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64A LEU* 4.0 24.9 - - + -
65A GLU 2.8 10.7 + - - +
66A VAL* 4.3 12.6 - - + -
67A GLY* 2.7 31.0 + - - -
87A ILE* 1.3 78.2 - - - +
89A GLU* 1.3 62.4 + - - +
112A LEU* 3.3 23.3 - - + +
114A GLY 3.3 20.2 - - - +
116A TRP* 4.0 22.9 - - + -
119A VAL* 4.1 23.1 - - + -
120A ALA* 4.3 7.2 - - + +
123A LEU* 4.3 11.0 - - + -
150A PHE* 5.5 0.4 - - + -
2001A SAH 3.9 11.2 + - + -
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Residues in contact with GLU 89 (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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68A PHE* 2.9 28.6 + - + +
87A ILE 4.0 0.2 + - - -
88A ILE* 1.3 75.7 - - - +
90A CYS* 1.3 55.0 + - - +
91A ASN* 3.2 32.2 + - - +
94A VAL* 3.6 10.8 - - + +
95A PHE* 3.7 20.4 - - + +
98A LEU* 4.3 18.4 - - + -
112A LEU 3.0 6.5 + - - -
113A LYS* 3.3 11.1 - - - +
114A GLY 2.8 27.0 + - - -
2001A SAH 2.5 44.7 + - - -
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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