Contacts of the strand formed by residues 102 - 111 (chain A) in PDB entry 1C8D
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 HIS 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A VAL 5.5 0.2 - - - -
83A VAL* 3.5 4.3 - - - +
84A VAL* 2.9 51.5 + - + +
100A ASP* 3.0 20.4 + - + +
101A ILE* 1.3 79.5 - - - +
103A ALA* 1.3 72.2 + - - +
104A GLU* 2.9 29.5 + - + +
211A TYR* 3.9 23.1 - + + -
214A TRP* 3.5 32.3 - - + -
233A TYR* 5.3 0.2 - - - -
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Residues in contact with ALA 103 (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 ARG* 5.9 2.2 - - + -
82A VAL 3.3 9.4 - - - +
83A VAL* 4.1 15.5 - - + +
102A HIS* 1.3 76.0 - - - +
104A GLU* 1.3 62.6 + - - +
211A TYR* 3.7 10.0 - - - -
212A PHE* 2.9 48.1 + - + +
213A GLN 4.3 2.5 - - - +
214A TRP* 3.4 18.2 - - + -
233A TYR* 4.3 2.0 - - - +
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Residues in contact with GLU 104 (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 ARG 3.8 0.2 - - - +
81A ARG* 3.8 2.8 - - - +
82A VAL* 2.8 43.7 + - + +
84A VAL* 5.1 4.6 - - + +
102A HIS* 2.9 30.3 + - + +
103A ALA* 1.3 77.5 - - - +
105A ILE* 1.3 63.9 + - - +
106A VAL* 3.7 17.8 + - + +
209A ARG* 3.6 29.4 - - + +
210A TYR 3.2 16.8 - - - +
211A TYR* 4.6 2.0 - - + -
212A PHE* 4.0 3.8 - - - +
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Residues in contact with ILE 105 (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 TYR* 4.2 22.4 - - + -
80A ARG 3.3 10.3 - - - +
81A ARG* 4.5 9.2 - - + -
104A GLU* 1.3 74.7 - - - +
106A VAL* 1.3 62.4 + - - +
107A THR* 3.6 2.3 + - + +
209A ARG* 3.3 7.4 - - - +
210A TYR* 2.8 65.7 + - + +
212A PHE* 3.4 37.7 - - + -
243A PHE* 3.4 30.5 - - + -
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Residues in contact with VAL 106 (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 GLU* 6.0 1.3 - - + +
78A ASN 4.0 2.0 - - - +
79A TYR* 3.4 7.1 - - - +
80A ARG* 2.8 52.5 + - + +
82A VAL* 4.2 20.0 - - + -
104A GLU* 3.7 24.2 - - + +
105A ILE* 1.3 72.3 - - - +
107A THR* 1.3 67.6 + - - +
207A PRO* 6.5 1.1 - - + -
208A TRP 5.0 2.0 - - - +
209A ARG* 4.3 6.1 - - + -
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Residues in contact with THR 107 (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 ASN 4.8 0.7 - - - -
79A TYR* 3.7 24.5 - - + -
105A ILE* 3.9 9.6 - - + +
106A VAL* 1.3 84.3 - - - +
108A PRO* 1.3 68.6 - - - +
109A TRP* 3.2 19.1 + - - +
207A PRO* 5.5 3.1 - - - +
208A TRP* 2.6 63.4 + - + +
210A TYR* 3.9 10.1 - - + -
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Residues in contact with PRO 108 (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 PRO* 3.8 19.4 - - + +
76A SER 3.4 25.4 - - - +
77A GLU* 4.0 19.5 - - - +
78A ASN 3.8 13.2 - - - +
79A TYR* 4.0 22.9 - - + -
107A THR* 1.3 85.4 - - - +
109A TRP* 1.3 68.3 + - + +
110A SER* 5.2 0.7 + - - -
247A GLU* 5.3 1.1 - - - +
501A LYS* 3.6 29.2 - - - +
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Residues in contact with TRP 109 (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 TYR* 3.8 16.5 + + - -
107A THR* 3.1 13.0 + - - +
108A PRO* 1.3 92.4 - - + +
110A SER* 1.3 57.5 + - - +
174A MET* 3.8 43.7 - - + -
176A ALA* 4.0 10.1 - - + -
207A PRO* 3.7 2.1 - - - +
208A TRP* 2.7 34.3 + - + +
246A ILE* 3.6 33.1 - - + +
247A GLU* 3.0 29.2 + - - -
252A VAL* 4.0 23.6 - - + -
499A PHE* 3.7 27.6 - - + -
500A VAL 3.8 6.7 - - - -
501A LYS* 3.6 29.7 - - + +
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Residues in contact with SER 110 (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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71A LEU* 3.7 24.4 - - - +
72A ASN 5.5 0.2 + - - -
108A PRO 5.2 0.7 + - - -
109A TRP* 1.3 75.6 + - - +
111A LEU* 1.3 60.5 - - - +
112A VAL 4.0 0.2 + - - -
205A PRO* 4.1 12.8 - - - -
206A THR 3.3 12.3 + - - -
207A PRO* 4.3 6.6 - - - +
208A TRP* 4.4 2.7 - - - -
499A PHE* 3.2 6.7 - - - +
500A VAL* 2.9 43.2 + - - +
501A LYS* 5.0 0.4 - - - +
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Residues in contact with LEU 111 (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 SER* 1.3 72.7 - - - +
112A VAL* 1.3 77.8 + - - +
113A ASP* 3.5 22.1 + - + +
186A THR* 3.5 34.5 - - - +
188A ALA* 4.6 8.1 - - + -
193A GLU 5.6 0.3 - - - +
205A PRO* 3.3 3.9 - - - +
206A THR* 2.7 40.0 + - - +
207A PRO 5.4 0.2 - - - +
208A TRP* 4.0 22.6 - - + +
497A GLN* 4.4 20.2 - - + +
498A LEU 3.9 9.9 - - - +
499A PHE* 4.4 8.3 - - + -
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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