Contacts of the strand formed by residues 79 - 85 (chain A) in PDB entry 7CE1
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 VAL 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ARG* 3.8 10.8 - - - +
71A ARG* 4.4 12.3 - - - +
77A THR* 3.0 29.2 + - - +
78A ASN* 1.3 79.8 - - - +
80A ILE* 1.3 72.1 + - - +
81A ALA* 4.5 2.2 - - + +
110A TYR* 3.6 1.8 - - - -
111A HIS* 3.6 9.0 - - + +
113A VAL* 3.5 32.3 - - + -
135A SER 3.7 18.4 - - - +
136A ALA* 3.7 1.8 - - + -
137A ASP* 2.9 32.3 + - - +
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Residues in contact with ILE 80 (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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79A VAL* 1.3 79.2 - - - +
81A ALA* 1.3 62.0 + - - +
101A ILE* 5.2 0.7 - - + -
105A LEU* 3.6 31.0 - - + -
110A TYR* 4.0 12.1 - - + -
111A HIS 2.8 13.6 + - - +
112A LEU* 3.2 24.4 - - + +
113A VAL 3.0 22.0 + - - -
138A GLY 3.6 3.4 - - - +
140A ILE* 4.0 15.5 - - + -
320A ALA* 5.3 2.5 - - - +
323A LEU* 3.6 35.9 - - + -
324A LEU* 3.7 23.1 - - + -
327A ILE* 4.3 7.9 - - + -
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Residues in contact with ALA 81 (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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79A VAL* 4.1 2.1 + - + -
80A ILE* 1.3 75.1 - - - +
82A LEU* 1.3 58.8 + - - +
113A VAL* 3.5 12.1 - - + +
115A THR* 4.5 9.2 - - + +
130A ILE* 3.8 29.4 - - + -
136A ALA* 3.9 15.9 - - + -
138A GLY 3.0 9.6 + - - +
139A VAL* 3.4 4.5 - - + +
140A ILE* 2.9 27.0 + - - +
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Residues in contact with LEU 82 (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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80A ILE 3.9 0.8 + - - -
81A ALA* 1.3 72.5 - - - +
83A VAL* 1.3 72.8 + - - +
84A LEU* 3.9 25.8 + - + -
97A MET* 5.0 12.1 - - + -
98A VAL* 4.2 23.1 - - + -
101A ILE* 4.0 21.3 - - + -
112A LEU* 4.2 17.7 - - + -
113A VAL 2.9 14.0 + - - +
114A VAL* 3.6 12.5 - - + +
115A THR* 3.1 22.3 + - - +
140A ILE* 3.7 33.0 - - + +
141A ILE 6.0 0.4 - - - -
142A SER* 6.5 0.9 - - - -
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Residues in contact with VAL 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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81A ALA 4.8 0.7 - - - +
82A LEU* 1.3 75.8 - - - +
84A LEU* 1.3 68.2 + - - +
115A THR* 3.1 28.0 - - - +
117A HIS* 4.7 4.6 - - + +
126A PRO* 4.4 8.7 - - + -
127A ILE* 4.2 18.4 - - + -
130A ILE* 4.0 20.0 - - + -
139A VAL* 4.2 9.2 - - + -
140A ILE 3.0 22.4 + - - +
141A ILE* 3.4 25.3 - - + -
142A SER* 4.4 9.2 + - - -
150A ARG* 4.4 8.7 - - - +
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Residues in contact with LEU 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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82A LEU* 4.2 30.7 - - + +
83A VAL* 1.3 83.9 - - - +
85A SER* 1.3 64.0 + - - +
94A THR* 4.0 28.0 - - + -
97A MET* 4.9 7.4 - - + -
98A VAL* 5.5 5.4 - - + -
114A VAL* 4.4 14.4 - - + -
115A THR 3.5 5.3 + - - -
116A PRO* 3.2 8.1 - - + +
117A HIS* 3.0 28.1 + - - -
142A SER* 4.9 9.6 - - - +
95B SER* 6.3 0.4 - - - -
98B VAL* 5.5 3.4 - - + -
99B PHE* 3.7 35.7 - - + -
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Residues in contact with SER 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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84A LEU* 1.3 75.0 - - - +
86A VAL* 1.3 64.2 + - - +
87A ASP* 2.9 26.7 + - - +
88A GLU* 4.7 3.3 - - - +
117A HIS* 3.2 31.8 - - - -
119A HIS* 5.7 3.6 - - - -
120A ALA* 5.9 0.9 - - - -
142A SER* 5.1 5.2 + - - -
143A LYS* 3.2 30.0 - - - +
99B PHE* 3.9 9.5 - - - -
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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