Contacts of the strand formed by residues 102 - 106 (chain I) in PDB entry 6AHU
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 102 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74I LEU* 5.3 1.3 - - + -
75I THR 4.3 2.6 + - - -
76I ARG* 3.5 65.7 - - + +
77I LEU 3.5 4.2 + - - -
100I TYR 3.2 4.0 - - - +
101I ASP* 1.3 86.5 - - + +
103I VAL* 1.3 64.8 + - - +
104I ALA* 5.2 2.0 - - + +
123I ASP* 3.4 9.9 - - + +
124I LEU* 3.7 31.2 - - + -
228I ALA* 3.7 22.4 - - + +
229I LEU* 4.5 8.7 - - + -
232I GLY* 4.8 1.8 - - - -
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Residues in contact with VAL 103 (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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77I LEU* 4.2 7.2 - - + +
79I ILE* 3.8 24.9 - - + -
90I LEU* 4.9 3.1 - - + -
99I LEU 5.2 1.6 - - - +
100I TYR* 3.3 25.4 - - + +
102I VAL* 1.3 72.4 - - - +
104I ALA* 1.3 61.3 + - - +
122I VAL* 3.9 19.6 - - + +
123I ASP* 2.8 38.5 + - - +
124I LEU 3.1 6.4 + - - +
235I ARG* 3.5 33.7 - - - +
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Residues in contact with ALA 104 (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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36I ASN* 5.8 1.6 - - - +
76I ARG* 6.2 2.2 - - + -
77I LEU 3.0 25.6 + - - +
78I THR* 3.4 4.1 - - - +
79I ILE* 3.1 21.6 + - - +
102I VAL* 4.1 2.4 + - + -
103I VAL* 1.3 76.1 - - - +
105I VAL* 1.3 61.1 + - - +
124I LEU* 3.3 15.0 - - + +
126I CYS* 3.8 12.6 - - - -
153I GLU* 3.4 26.0 - - - +
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Residues in contact with VAL 105 (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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79I ILE* 3.6 5.6 - - + +
81I VAL* 3.8 28.0 - - + -
87I CYS* 6.2 0.2 - - - -
90I LEU* 3.9 18.8 - - + -
104I ALA* 1.3 74.1 - - - +
106I PHE* 1.3 60.0 + - - +
107I PRO* 3.4 11.9 - - + +
112I LEU* 5.9 2.5 - - + -
116I ALA* 4.7 9.9 - - + -
120I LEU* 4.2 13.2 - - + -
122I VAL* 3.8 35.2 - - + +
124I LEU 3.2 6.3 + - - +
125I VAL* 3.6 5.0 - - + -
126I CYS* 2.7 33.9 + - - -
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Residues in contact with PHE 106 (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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10I ARG* 5.9 0.4 - - - -
78I THR* 5.1 2.2 - - + -
79I ILE 2.7 17.2 + - - +
80I ILE* 3.7 29.4 - - + -
81I VAL* 3.0 28.8 + - - +
105I VAL* 1.3 77.0 - - - +
107I PRO* 1.3 66.8 - - - +
108I LYS* 3.6 30.3 - - + -
126I CYS* 3.2 31.0 - - + -
127I ILE* 4.6 0.2 - - - -
128I THR* 3.2 47.6 - - - -
133I LEU* 4.4 15.9 - - + -
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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