Contacts of the strand formed by residues 71 - 78 (chain I) in PDB entry 6D6Q
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 71 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I PRO* 5.2 3.8 - - + -
69I ALA* 5.2 3.6 - - + -
70I ILE* 1.3 75.6 - - - +
72I THR* 1.3 70.7 + - - +
87I ILE* 3.5 26.0 - - + -
89I TYR 3.1 19.5 - - - +
90I VAL* 3.8 15.7 - - + -
91I GLY 4.4 0.4 - - - +
129I LEU* 3.3 1.9 - - - -
130I ALA 2.9 38.1 + - - +
132I VAL* 3.7 29.4 - - + +
144I LEU* 3.9 15.8 - - + +
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Residues in contact with THR 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I ILE 5.6 0.7 - - - +
71I VAL* 1.3 87.7 - - - +
73I CYS* 1.3 67.5 + - - +
87I ILE* 4.0 1.0 - - - +
88I LEU* 3.7 12.0 + - - +
89I TYR* 2.9 46.9 + - + +
91I GLY 5.1 6.3 - - - +
127I ILE* 4.6 10.8 - - + -
128I VAL 3.2 9.9 - - - +
129I LEU* 3.8 20.6 - - + +
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Residues in contact with CYS 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I VAL 4.8 0.9 - - - -
72I THR* 1.3 79.7 + - - +
74I LYS* 1.3 58.7 + - - +
85I VAL* 3.7 32.3 - - + -
86I HIS 3.1 20.2 - - - +
87I ILE* 4.2 5.4 - - + -
88I LEU* 4.4 7.4 - - - +
103I ILE* 4.8 0.9 - - - -
127I ILE* 3.3 8.6 - - - +
128I VAL* 2.9 57.8 + - - +
129I LEU* 5.2 0.4 - - - -
144I LEU* 3.8 16.6 - - - -
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Residues in contact with LYS 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D PHE* 3.2 40.0 - - + -
73I CYS* 1.3 75.8 - - - +
75I VAL* 1.3 68.1 + - - +
76I SER* 3.3 10.0 + - - +
85I VAL* 3.1 23.3 - - - -
86I HIS* 3.2 10.9 + - + +
88I LEU* 4.3 19.5 - - + -
125I GLY* 3.5 23.2 - - - +
126I ASP 3.5 12.8 - - - +
127I ILE* 4.7 14.8 - - + -
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Residues in contact with VAL 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I LYS* 1.3 73.9 + - - +
76I SER* 1.3 57.6 + - - +
77I SER 4.3 3.6 - - - +
78I ILE* 3.7 28.0 - - + -
83I ALA* 4.6 3.8 - - + -
84I LYS 4.4 1.8 - - - +
85I VAL* 3.9 16.4 - - + -
122I PHE* 4.4 18.8 - - + -
123I ARG 3.2 15.9 - - - +
124I PRO* 3.1 2.0 - - + +
125I GLY* 2.5 34.0 + - - -
126I ASP* 2.9 35.6 + - - +
128I VAL* 4.3 19.3 - - + -
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Residues in contact with SER 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D PHE* 4.3 34.2 - - - +
113D ARG* 6.2 0.3 - - - -
74I LYS* 3.3 9.6 + - - +
75I VAL* 1.3 73.1 - - - +
77I SER* 1.3 63.2 + - - +
84I LYS* 3.3 10.9 + - - -
86I HIS* 3.0 36.5 + - - -
100I ARG* 5.5 2.0 - - - -
124I PRO* 3.1 24.1 - - - +
125I GLY 4.9 0.2 - - - +
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Residues in contact with SER 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ARG* 5.8 6.6 - - - +
75I VAL* 4.3 0.3 - - - +
76I SER* 1.3 79.6 - - - +
78I ILE* 1.3 78.3 + - - +
83I ALA* 3.4 0.5 - - - +
84I LYS* 2.9 53.6 + - - +
100I ARG* 5.2 3.1 - - - -
124I PRO* 5.2 0.2 - - - -
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Residues in contact with ILE 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173G ASP* 3.5 44.3 + - + +
174G MET* 4.2 16.4 - - + +
175G GLU 5.6 0.5 + - - -
75I VAL* 3.7 24.2 - - + -
77I SER* 1.3 88.1 + - - +
79I ASN* 1.3 65.4 + - - +
82I PHE 3.5 7.2 - - - -
83I ALA* 3.8 12.1 - - + +
118I ILE* 4.3 17.7 - - + -
119I TYR* 4.8 10.1 - - + -
122I PHE* 4.8 10.5 - - + +
123I ARG 4.7 1.1 - - - -
124I PRO* 4.2 14.6 - - + -
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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