Contacts of the strand formed by residues 77 - 82 (chain X) in PDB entry 3FEW
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 VAL 77 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70X TYR 4.0 3.1 - - - +
71X VAL* 4.0 20.2 - - + -
76X GLN* 1.3 73.1 - - - +
78X ARG* 1.3 65.9 + - - +
79X ILE* 4.0 4.4 + - + -
88X THR* 3.6 20.6 - - - +
90X VAL* 3.9 23.1 - - + -
209X PRO* 4.6 4.5 - - + +
212X VAL* 3.9 20.4 - - + +
214X LYS 3.2 6.1 + - - -
215X PHE* 3.4 33.7 - - + +
216X ASP 2.9 24.7 + - - +
291X VAL* 4.4 4.0 - - + -
295X PHE* 6.0 0.7 - - + -
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Residues in contact with ARG 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X PRO* 4.0 24.2 - - - +
69X PRO* 4.0 12.5 + - - +
70X TYR 5.0 2.6 + - - -
72X ASP* 2.9 48.9 + - - +
76X GLN* 4.0 0.9 + - + +
77X VAL* 1.3 73.5 - - - +
79X ILE* 1.3 60.6 + - - +
80X THR* 5.9 1.6 - - - +
88X THR* 2.7 30.5 + - - -
89X PRO* 3.3 29.0 - - + +
102X VAL* 5.0 5.0 + - - +
103X GLN 5.8 0.2 - - - -
216X ASP* 3.5 21.5 + - + +
223X HIS* 6.1 3.1 - - - -
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Residues in contact with ILE 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77X VAL* 4.3 5.2 - - + +
78X ARG* 1.3 79.8 - - - +
80X THR* 1.3 72.9 + - - +
81X ILE* 4.5 0.9 - - + -
86X VAL* 3.8 17.9 - - + -
87X LYS 3.3 9.9 - - - +
88X THR* 4.3 3.8 - - - -
89X PRO* 5.4 0.2 - - - -
103X GLN 5.6 0.2 - - - -
215X PHE* 3.9 15.9 - - + -
216X ASP 2.9 7.6 + - - +
217X VAL* 3.3 29.7 - - + -
218X ASP* 2.8 26.9 + - - +
287X ALA* 3.8 9.2 - - + +
288X ALA* 3.7 25.8 - - - +
291X VAL* 3.5 29.6 - - + -
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Residues in contact with THR 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78X ARG* 5.9 1.6 - - - +
79X ILE* 1.3 79.0 + - - +
81X ILE* 1.3 67.2 + - - +
82X THR* 3.9 7.4 + - - +
85X LEU 3.5 1.7 - - - +
86X VAL* 3.7 0.5 - - - -
87X LYS* 2.8 36.5 + - - +
103X GLN* 3.9 49.7 + - + +
218X ASP* 3.7 30.3 - - - +
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Residues in contact with ILE 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79X ILE* 4.5 0.4 - - + -
80X THR* 1.3 78.5 - - - +
82X THR* 1.3 61.8 + - - +
83X ASN 4.2 0.8 + - - +
84X GLY* 3.9 27.1 - - - +
85X LEU 3.2 8.5 - - - +
86X VAL* 4.1 10.1 - - + -
217X VAL* 4.0 6.7 - - + -
218X ASP* 3.1 14.4 + - - +
219X VAL* 3.6 32.1 - - + -
220X GLU 4.7 9.2 + - - -
283X GLN* 3.9 30.3 - - + +
287X ALA* 3.7 29.8 - - + -
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Residues in contact with THR 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80X THR* 4.1 4.9 + - - +
81X ILE* 1.3 74.1 + - - +
83X ASN* 1.3 87.1 + - - +
84X GLY 3.2 0.7 - - - -
85X LEU* 2.9 27.4 + - - +
87X LYS* 4.7 7.1 - - - +
103X GLN* 3.0 35.5 + - - +
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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