Contacts of the strand formed by residues 106 - 114 (chain A) in PDB entry 1F4J
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 LYS 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A TYR* 4.2 18.2 - - + -
85A PHE 3.0 4.9 - - - +
86A GLU* 3.8 35.2 - - + +
104A GLY 3.5 14.7 + - - -
105A LYS* 1.3 83.2 - - - +
107A THR* 1.3 65.4 + - - +
108A PRO* 4.3 3.9 - - - +
380A ARG* 4.5 10.4 + - - -
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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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84A TYR* 3.1 3.1 - - - -
85A PHE* 2.6 45.4 + - - -
99A VAL* 3.7 28.2 + - - +
105A LYS* 4.3 8.0 + - - +
106A LYS* 1.3 76.2 + - - +
108A PRO* 1.3 75.0 - - + +
109A ILE* 3.4 1.9 - - - +
136A PHE* 4.1 9.6 - - + -
137A TYR 3.3 35.0 - - - +
138A THR* 4.0 7.7 - - + +
139A GLU* 5.1 1.0 + - - -
380A ARG* 4.4 4.6 + - - +
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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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83A GLY 3.5 10.1 - - - +
84A TYR* 4.0 2.9 - - + -
106A LYS 4.3 2.0 - - - +
107A THR* 1.3 95.0 - - + +
109A ILE* 1.3 62.0 + - - +
137A TYR* 3.0 33.9 + - + +
379A TYR* 3.5 19.7 - - - +
380A ARG* 3.6 35.4 - - - +
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Residues in contact with ILE 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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82A PHE* 3.5 7.8 - - - +
83A GLY 2.9 34.3 + - - +
84A TYR 3.5 28.5 - - - +
85A PHE* 3.7 7.6 - - + +
107A THR 3.4 11.4 + - - +
108A PRO* 1.3 81.0 - - - +
110A ALA* 1.3 60.6 + - - +
111A VAL* 4.0 17.7 - - + -
134A VAL* 4.2 5.4 - - + -
135A LYS 3.0 10.1 - - - +
136A PHE* 3.8 27.6 - - + -
137A TYR* 3.8 4.1 - - - -
316A LEU* 3.7 23.8 - - + -
317A VAL 4.2 1.8 - - - +
318A LEU* 4.1 11.7 - - + -
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Residues in contact with ALA 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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81A ALA 3.7 5.8 - - - -
82A PHE* 3.7 16.8 - - + -
109A ILE* 1.3 72.7 - - - +
111A VAL* 1.3 66.2 + - - +
134A VAL* 3.5 0.2 - - - -
135A LYS* 2.8 36.6 + - + +
137A TYR* 3.2 28.5 - - + +
332A ILE* 3.8 18.4 - - + -
334A PHE* 3.7 2.8 - - - -
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Residues in contact with VAL 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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79A ALA 4.6 0.2 - - - -
80A GLY* 3.2 3.5 - - - -
81A ALA 3.0 32.5 + - - +
82A PHE* 5.9 0.2 - - - -
109A ILE* 4.0 13.2 - - + -
110A ALA* 1.3 81.4 - - - +
112A ARG* 1.3 67.9 + - - +
113A PHE* 4.0 18.2 - - + -
132A PHE* 3.8 26.5 - - + -
133A ALA 3.2 15.0 - - - +
134A VAL* 3.9 15.9 - - + -
316A LEU* 6.0 0.4 - - + -
318A LEU* 3.8 28.0 - - + -
332A ILE* 5.7 2.1 - - - +
334A PHE* 4.2 2.5 - - - -
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Residues in contact with ARG 112 (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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72A ARG* 3.1 39.5 - - - +
75A HIS 2.9 29.5 + - - -
76A ALA 3.1 19.4 + - - -
78A GLY* 3.7 12.9 - - - +
79A ALA 3.2 10.1 - - - +
80A GLY* 4.7 0.7 - - - -
111A VAL* 1.3 80.2 - - - +
113A PHE* 1.3 67.5 + - - +
114A SER* 3.7 15.9 + - - -
131A GLY 3.6 2.8 - - - +
132A PHE* 3.8 0.2 - - - -
133A ALA* 3.1 29.4 + - - +
325A TYR* 5.1 1.8 + - - -
329A VAL* 3.9 20.9 - - + +
330A GLU* 5.1 1.6 + - - +
332A ILE* 3.6 12.3 - - + -
334A PHE* 3.8 16.3 - - + -
600A HEM 2.9 28.4 + - - +
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Residues in contact with PHE 113 (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 GLY* 3.3 1.7 - - - -
79A ALA 2.8 28.7 + - - +
80A GLY* 5.7 0.2 - - - -
81A ALA* 5.6 0.2 - - + -
111A VAL* 4.0 8.1 - - + -
112A ARG* 1.3 77.0 - - - +
114A SER* 1.3 68.1 + - - +
131A GLY 3.0 11.0 - - - +
132A PHE* 3.4 40.8 - + - -
209A HIS* 3.2 43.3 - + + +
212A MET* 3.3 25.6 - - + -
265A LEU* 3.7 30.1 - - + -
277A TRP* 3.5 28.7 - + - -
318A LEU* 3.9 13.9 - - + -
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Residues in contact with SER 114 (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 HIS* 3.0 28.7 + - - +
77A LYS 3.1 17.7 - - - -
78A GLY* 4.2 0.7 - - - -
112A ARG* 3.7 17.0 + - - -
113A PHE* 1.3 81.2 - - - +
115A THR* 1.3 65.9 + - - +
130A ARG* 3.0 15.2 - - - +
131A GLY* 2.7 33.6 + - - -
209A HIS* 4.2 6.5 - - - -
600A HEM 4.4 2.3 - - - +
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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