Contacts of the strand formed by residues 96 - 104 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ILE 3.7 4.5 - - - -
54A GLU* 4.1 6.3 - - + +
87A GLN* 4.3 6.2 + - - -
89A VAL* 4.1 14.1 - - - +
92A CYS* 5.2 0.4 - - - -
94A ASP 3.8 2.1 + - - +
95A PRO* 1.3 71.1 - - - +
97A PHE* 1.3 64.6 + - - +
98A HIS* 3.8 22.2 - - + +
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Residues in contact with PHE 97 (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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37A LEU* 4.3 9.9 - - + -
52A ILE* 3.5 31.6 - - + +
53A ILE 2.8 7.7 + - - +
54A GLU* 4.2 7.0 - - - -
55A GLY* 4.4 0.4 - - - -
58A LEU* 5.9 0.2 - - + -
68A PRO* 3.7 18.4 - - + -
69A TYR* 4.0 0.4 - - - -
70A VAL* 3.7 20.6 - - + -
86A THR* 3.4 27.6 - - + -
87A GLN* 3.7 22.7 + - + +
89A VAL* 3.6 24.2 - - + -
95A PRO* 3.5 36.1 - - + -
96A ALA* 1.3 71.2 - - - +
98A HIS* 1.3 72.7 + - - +
99A GLU* 3.2 18.7 - - + +
118A VAL* 5.6 1.6 - - + -
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Residues in contact with HIS 98 (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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51A HIS* 4.3 15.1 + - - +
52A ILE 3.1 4.8 + - - -
53A ILE* 2.8 40.8 + - + +
54A GLU* 5.5 3.3 - - + +
96A ALA* 3.8 28.4 - - + +
97A PHE* 1.3 74.7 - - - +
99A GLU* 1.3 59.5 + - - +
100A HIS* 4.9 4.6 - - - -
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Residues in contact with GLU 99 (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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50A LEU 3.9 0.2 - - - +
51A HIS* 3.5 2.3 - - - -
52A ILE 2.9 32.1 + - - +
85A LYS 4.2 1.4 - - - +
86A THR* 3.2 24.4 - - + -
87A GLN* 2.6 47.5 + - - +
97A PHE* 3.2 16.1 - - + +
98A HIS* 1.3 77.6 - - - +
100A HIS* 1.3 65.5 + - - +
101A PHE* 3.8 22.0 - - + -
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Residues in contact with HIS 100 (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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49A LEU* 4.3 19.0 - - + +
50A LEU 3.3 4.0 - - - +
51A HIS* 3.4 49.1 + + + +
98A HIS 4.9 3.8 - - - -
99A GLU* 1.3 76.6 - - - +
101A PHE* 1.3 69.4 + - - +
102A PHE* 4.7 12.5 - - + -
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Residues in contact with PHE 101 (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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48A LEU 3.5 0.2 - - - +
49A LEU* 3.4 9.5 - - - +
50A LEU* 2.7 47.1 + - + +
52A ILE* 3.6 25.1 - - + -
72A ILE* 4.2 9.4 - - + -
84A GLN* 3.3 31.9 - - + +
85A LYS* 3.2 45.3 - - - -
86A THR* 3.5 26.0 - - + -
99A GLU* 3.8 22.4 - - + -
100A HIS* 1.3 78.3 - - - +
102A PHE* 1.3 65.9 + - - +
103A PHE* 4.0 2.2 - - + +
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Residues in contact with PHE 102 (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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47A VAL* 4.3 20.9 - - + -
48A LEU 3.3 4.7 - - - -
49A LEU* 3.7 38.1 - - + -
84A GLN* 3.1 19.4 + - - +
100A HIS* 4.7 12.8 - - + -
101A PHE* 1.3 78.0 - - - +
103A PHE* 1.3 60.7 - - - +
104A PRO* 3.3 10.7 - - + +
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Residues in contact with PHE 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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47A VAL* 4.7 0.7 - - - -
48A LEU* 2.7 40.5 + - + +
50A LEU* 4.0 18.6 - - + -
72A ILE* 3.8 37.2 - - + -
73A SER* 4.0 7.9 - - - -
74A LEU* 3.5 38.1 - - + -
82A ARG* 3.0 49.6 - - + -
84A GLN* 3.7 15.3 - - + +
101A PHE* 4.0 2.2 - - + -
102A PHE* 1.3 72.3 - - - +
104A PRO* 1.3 72.7 - - + +
105A VAL* 4.2 7.9 - - + -
114A LEU* 4.6 3.6 - - + -
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Residues in contact with PRO 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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46A ARG 3.7 9.6 - - - +
47A VAL* 4.2 15.9 - - + -
82A ARG* 2.8 21.2 + - - +
84A GLN* 4.9 2.2 - - - +
102A PHE* 3.3 13.9 - - + +
103A PHE* 1.3 88.6 - - + +
105A VAL* 1.3 60.2 + - - +
126B ARG* 5.3 0.9 + - - -
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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