Contacts of the strand formed by residues 96 - 104 (chain B) in PDB entry 3FBK
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 ALA 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B ILE 3.7 4.9 - - - -
54B GLU* 4.1 5.8 - - + +
87B GLN* 4.3 5.9 + - - -
89B VAL* 4.2 13.7 - - - +
92B CYS* 5.2 0.4 - - - -
94B ASP 3.8 2.6 + - - +
95B PRO* 1.3 70.9 - - - +
97B PHE* 1.3 63.3 + - - +
98B HIS* 3.8 23.2 - - + +
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Residues in contact with PHE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 4.3 10.1 - - + -
52B ILE* 3.5 31.9 - - + +
53B ILE 2.8 8.5 + - - -
54B GLU* 4.2 7.0 - - - -
55B GLY 4.4 0.4 - - - -
58B LEU* 5.9 0.2 - - + -
68B PRO* 3.8 18.6 - - + -
69B TYR* 4.0 0.7 - - - -
70B VAL* 3.7 19.3 - - + -
86B THR* 3.4 29.4 - - + -
87B GLN* 3.7 23.0 + - + +
89B VAL* 3.7 22.4 - - + -
95B PRO* 3.5 36.1 - - + -
96B ALA* 1.3 72.7 - - - +
98B HIS* 1.3 72.1 - - - +
99B GLU* 3.2 17.7 - - - +
118B VAL* 5.6 1.3 - - + -
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Residues in contact with HIS 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B HIS* 4.3 15.1 + - - +
52B ILE 3.1 4.8 + - - -
53B ILE* 2.8 42.1 + - + +
54B GLU* 5.4 3.9 - - + +
96B ALA* 3.8 27.3 - - + +
97B PHE* 1.3 74.3 - - - +
99B GLU* 1.3 59.7 + - - +
100B HIS* 4.9 4.6 - - - -
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Residues in contact with GLU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU 3.9 0.3 - - - +
51B HIS* 3.6 2.2 - - - -
52B ILE* 2.9 31.2 + - - +
85B LYS 4.2 1.6 - - - +
86B THR* 3.2 25.1 - - + -
87B GLN* 2.7 48.3 + - - +
97B PHE* 3.2 16.0 - - + +
98B HIS* 1.3 78.4 - - - +
100B HIS* 1.3 65.1 + - - +
101B PHE* 3.8 21.9 - - + -
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Residues in contact with HIS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 4.3 19.0 - - + +
50B LEU 3.3 4.3 - - - +
51B HIS* 3.4 48.8 + + + +
98B HIS 4.9 4.0 - - - -
99B GLU* 1.3 76.6 - - - +
101B PHE* 1.3 70.8 + - - +
102B PHE* 4.7 12.3 - - + -
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Residues in contact with PHE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU 3.5 0.2 - - - +
49B LEU* 3.4 10.0 - - - +
50B LEU* 2.7 47.6 + - + +
52B ILE* 3.6 24.5 - - + -
72B ILE* 4.2 9.4 - - + -
84B GLN* 3.3 31.2 - - + +
85B LYS* 3.2 45.3 - - - -
86B THR* 3.5 25.4 - - + -
99B GLU* 3.8 23.3 - - + -
100B HIS* 1.3 80.1 - - - +
102B PHE* 1.3 66.7 + - - +
103B PHE* 4.0 2.2 - - + +
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B VAL* 4.3 21.1 - - + -
48B LEU 3.3 6.1 - - - -
49B LEU* 3.7 37.7 - - + -
84B GLN* 3.1 19.7 + - - -
100B HIS* 4.7 13.0 - - + -
101B PHE* 1.3 78.4 - - - +
103B PHE* 1.3 60.0 + - - +
104B PRO* 3.3 10.7 - - + +
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B VAL* 4.6 0.2 - - - -
48B LEU* 2.7 41.3 + - + +
50B LEU* 4.0 18.6 - - + -
72B ILE* 3.8 37.9 - - + -
73B SER* 4.0 8.1 - - - -
74B LEU* 3.5 37.9 - - + -
82B ARG* 3.0 49.1 - - + -
84B GLN* 3.7 17.0 - - + +
101B PHE* 5.8 1.3 - - + -
102B PHE* 1.3 72.7 - - - +
104B PRO* 1.3 74.1 - - + +
105B VAL* 4.2 7.2 - - + -
114B LEU* 4.6 3.1 - - + -
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Residues in contact with PRO 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ARG* 5.3 1.0 + - - -
46B ARG 3.7 9.9 - - - +
47B VAL* 4.2 16.2 - - + -
82B ARG* 2.8 21.5 + - - +
84B GLN* 4.9 2.9 - - - +
102B PHE* 3.3 13.0 - - + +
103B PHE* 1.3 88.6 - - + +
105B VAL* 1.3 59.6 + - - +
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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