Contacts of the strand formed by residues 69 - 75 (chain A) in PDB entry 5FN3
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 ASP 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A GLN 5.8 0.2 - - - -
64A SER* 3.1 11.4 + - - +
65A SER* 3.3 32.4 + - - +
68A GLY* 1.3 80.9 - - - +
70A THR* 1.3 60.8 + - - +
95A MET* 3.2 20.8 - - + +
119A ALA* 4.2 18.8 - - + +
178A PHE* 5.6 2.6 - - - +
179A PRO* 4.3 20.4 - - + +
216A GLN* 4.1 2.5 - - - -
217A LEU 3.3 13.9 + - - +
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Residues in contact with THR 70 (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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68A GLY 4.2 0.6 - - - -
69A ASP* 1.3 74.9 - - - +
71A GLY* 1.3 67.2 + - - +
93A PRO* 4.3 9.6 - - + +
95A MET* 4.3 3.6 - - - -
119A ALA* 3.5 20.3 - - - +
214A ALA* 4.8 0.5 - - - +
215A MET 3.3 12.4 + - - -
216A GLN* 3.9 14.4 - - - +
661A PHE* 3.4 22.6 - - - -
663A ILE* 4.9 13.8 - - + +
144C PRO* 4.9 10.9 - - + +
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Residues in contact with GLY 71 (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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70A THR* 1.3 86.7 + - - +
72A VAL* 1.3 64.9 + - - -
93A PRO* 3.3 17.9 - - - -
95A MET* 3.9 9.2 - - - +
214A ALA* 3.1 5.9 - - - -
215A MET 2.8 32.6 + - - +
663A ILE* 6.1 1.6 - - - -
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Residues in contact with VAL 72 (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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71A GLY* 1.3 70.9 - - - -
73A ILE* 1.3 59.9 + - - +
91A ASN* 3.7 30.3 - - + +
93A PRO 3.5 2.4 + - - +
94A TYR* 3.2 34.1 - - + +
95A MET 2.8 20.1 + - - -
200A ASN* 3.2 28.5 - - + +
212A LEU* 3.8 31.0 - - + -
213A CYS 3.4 7.9 - - - +
214A ALA* 3.8 5.9 - - + +
663A ILE* 4.9 5.1 - - + +
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Residues in contact with ILE 73 (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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71A GLY 4.1 0.2 - - - +
72A VAL* 1.3 76.6 - - - +
74A HIS* 1.3 65.9 + - - +
75A VAL* 5.8 2.0 - - + -
94A TYR* 4.1 2.8 - - - -
95A MET* 3.1 10.5 - - + +
96A VAL 6.2 0.4 - - - -
97A LEU* 6.4 2.2 - - + -
192A ILE* 3.5 35.4 - - + +
196A TYR* 3.6 19.0 - - + -
200A ASN* 3.0 24.2 + - - +
213A CYS* 2.8 40.5 + - - +
214A ALA* 3.7 4.3 - - - -
215A MET* 3.3 47.1 - - + +
660A ILE* 3.9 4.9 - - + -
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Residues in contact with HIS 74 (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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73A ILE* 1.3 78.6 + - - +
75A VAL* 1.3 83.1 + - - +
76A VAL* 3.6 9.0 - - + +
81A ASP* 3.7 19.7 - - + +
84A TRP* 3.2 36.7 + + - -
85A VAL* 3.4 25.4 - - + -
94A TYR* 3.8 17.0 - - + -
95A MET 2.8 9.6 + - - +
96A VAL* 3.2 6.2 - - + +
97A LEU* 2.8 24.9 + - - +
196A TYR* 3.2 31.7 + - - -
200A ASN* 5.0 2.8 + - - +
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Residues in contact with VAL 75 (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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73A ILE* 5.8 2.9 - - + +
74A HIS* 1.3 91.1 + - - +
76A VAL* 1.3 58.2 + - - +
77A GLU* 3.7 27.8 - - + +
81A ASP* 3.5 11.3 - - - +
97A LEU* 3.5 21.5 - - + +
193A LYS* 4.0 31.2 - - + -
196A TYR* 3.9 39.3 + - + +
197A GLN* 5.4 2.5 - - - +
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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