Contacts of the strand formed by residues 212 - 218 (chain A) in PDB entry 5FN2
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 LEU 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A VAL* 3.7 21.1 - - + -
91A ASN* 4.0 17.3 - - + +
199A HIS* 4.5 0.4 - - - -
200A ASN* 3.1 26.5 - - - +
208A PRO* 4.0 22.0 - - + -
209A THR 3.1 24.0 - - - +
210A PHE* 3.4 42.8 - - + -
211A PRO* 1.3 74.0 - - - +
213A CYS* 1.3 60.6 + - - +
214A ALA 3.6 0.2 + - - -
662A LEU* 3.1 4.3 - - - -
663A ILE* 2.8 47.0 + - + +
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Residues in contact with CYS 213 (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 VAL* 3.3 5.4 - - - +
73A ILE* 2.8 44.4 + - + -
195A CYS* 2.0 62.4 - - - +
199A HIS* 4.0 4.7 - - + +
200A ASN* 2.8 26.5 + - - +
211A PRO 3.7 2.4 + - - -
212A LEU* 1.3 69.5 - - - +
214A ALA* 1.3 61.1 + - - +
660A ILE* 3.6 9.9 - - - -
661A PHE 3.6 4.0 - - - -
662A LEU* 4.0 3.5 - - - +
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Residues in contact with ALA 214 (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* 4.9 1.3 - - - +
71A GLY 3.0 18.2 - - - +
72A VAL* 3.6 9.0 - - - +
73A ILE* 3.8 1.3 - - - +
212A LEU 4.0 6.3 - - - +
213A CYS* 1.3 79.5 - - - +
215A MET* 1.3 60.4 + - - +
660A ILE* 3.7 4.0 - - - -
661A PHE* 2.8 63.2 + - + +
663A ILE* 4.4 9.4 - - + -
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Residues in contact with MET 215 (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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44A LEU* 3.5 29.6 - - + -
70A THR* 3.6 0.9 + - - -
71A GLY* 2.8 32.7 + - - +
73A ILE* 3.5 22.4 - - + +
95A MET* 3.6 34.1 - - + +
96A VAL 5.0 0.7 - - - +
97A LEU* 5.1 1.6 - - + -
122A ALA* 3.6 34.3 - - + +
181A PHE* 6.0 1.3 - - - -
183A LEU* 5.7 3.1 - - - -
192A ILE* 4.3 5.4 - - - -
214A ALA* 1.3 72.9 - - - +
216A GLN* 1.3 76.0 + - - +
217A LEU* 4.5 8.5 - - + +
658A ALA* 4.6 7.2 - - - -
659A ARG 3.8 6.5 - - - +
660A ILE* 3.9 10.5 - - + +
661A PHE* 4.5 0.4 - - - -
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Residues in contact with GLN 216 (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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41A TYR* 3.9 0.2 - - - -
67A SER 2.6 29.3 + - - -
68A GLY* 3.7 8.2 + - - +
69A ASP 3.5 14.8 - - - +
70A THR* 4.1 5.8 - - - -
95A MET* 5.0 0.2 - - - -
215A MET* 1.3 75.5 - - - +
217A LEU* 1.3 62.3 + - - +
218A PHE* 3.5 21.4 - - - -
657A ARG 4.3 0.2 - - - +
658A ALA* 3.3 2.8 - - - +
659A ARG* 2.6 77.1 + - - +
661A PHE* 3.3 28.2 - - + -
144C PRO* 4.0 12.5 - - + +
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Residues in contact with LEU 217 (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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64A SER* 3.6 4.7 + - - -
69A ASP* 2.9 29.3 + - - +
95A MET* 3.4 31.6 - - + -
121A LEU 4.5 3.6 - - - +
179A PRO* 3.5 36.1 - - + +
181A PHE* 3.3 58.1 - - + +
215A MET* 4.6 11.7 - - + -
216A GLN* 1.3 77.6 - - - +
218A PHE* 1.3 63.5 + - - +
219A SER* 3.7 5.6 - - - +
657A ARG 3.8 2.7 - - - -
658A ALA* 4.3 7.4 - - + +
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Residues in contact with PHE 218 (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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64A SER* 4.3 2.5 - - - +
65A SER 5.4 0.7 - - - +
66A ILE* 6.0 3.6 - - + -
67A SER* 4.0 9.4 - - - +
68A GLY* 3.4 26.7 - - - +
181A PHE* 4.5 0.9 - - - -
216A GLN* 3.5 29.2 - - + -
217A LEU* 1.3 79.8 - - - +
219A SER* 1.3 60.0 + - - +
220A HIS* 3.9 6.7 - - + +
655A ASP 4.5 7.2 - - - +
656A ILE* 3.1 5.7 - - - +
657A ARG* 2.8 98.4 + - + +
659A ARG* 3.5 29.4 - - + -
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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