Contacts of the strand formed by residues 78 - 87 (chain C) 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 GLY 78 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ALA 3.4 1.2 + - - -
77C LYS* 1.3 79.2 - - - +
79C ALA* 1.3 60.4 + - - -
112C ARG* 3.3 20.0 - - - +
113C PHE 3.2 11.0 - - - -
114C SER* 4.3 0.9 - - - -
124C ASP* 6.0 0.2 - - - -
209C HIS* 5.5 0.7 - - - -
262C ILE* 3.6 19.3 - - - +
325C TYR* 2.6 28.1 + - - -
329C VAL* 4.8 0.2 - - - -
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Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C GLY* 1.3 75.8 - - - +
80C GLY* 1.3 60.2 + - - +
112C ARG* 3.2 3.1 - - - +
113C PHE* 2.8 36.8 + - - +
209C HIS* 3.7 31.2 - - + +
262C ILE* 3.8 26.5 - - + -
265C LEU* 4.2 9.4 - - + -
325C TYR* 4.5 3.6 - - - -
329C VAL* 4.2 3.6 - - - -
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Residues in contact with GLY 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ALA* 1.3 75.4 - - - +
81C ALA* 1.3 63.5 - - - +
82C PHE* 4.8 1.1 - - - -
111C VAL 3.3 9.9 - - - -
112C ARG* 4.4 0.9 - - - -
265C LEU* 3.9 7.5 - - - +
321C ASN* 4.4 2.8 + - - -
322C PRO* 3.3 23.1 - - - +
325C TYR* 4.6 2.2 - - - -
329C VAL* 3.8 27.8 - - - +
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C GLY* 1.3 76.3 - - - +
82C PHE* 1.3 74.7 + - - +
111C VAL* 2.8 32.7 + - + +
113C PHE* 5.4 0.6 - - + -
265C LEU* 3.9 9.2 - - + -
269C ILE* 3.6 29.2 - - + -
318C LEU* 3.9 23.3 - - + -
320C ARG 3.6 5.4 - - - -
322C PRO* 4.4 0.9 - - - -
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Residues in contact with PHE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C GLY* 4.8 0.7 - - - -
81C ALA* 1.3 84.4 - - - +
83C GLY* 1.3 59.9 + - - +
109C ILE 3.4 8.1 - - - +
110C ALA* 3.6 30.1 - - + -
111C VAL 5.7 0.9 - - - -
137C TYR* 4.7 3.8 - + - -
318C LEU* 3.6 8.6 - - - -
319C ASN* 3.0 7.2 + - - -
320C ARG* 2.8 79.8 + - - +
321C ASN 4.3 0.2 - - - -
322C PRO* 3.7 18.8 - - + -
328C GLU* 3.4 52.5 - - + -
329C VAL* 5.1 1.3 - - + -
332C ILE* 4.9 2.7 - - + -
375C VAL* 4.3 13.9 - - + -
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Residues in contact with GLY 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PHE* 1.3 77.0 - - - +
84C TYR* 1.3 63.7 + - - +
108C PRO* 3.3 8.0 - - - +
109C ILE* 2.7 34.2 + - - +
317C VAL 3.1 11.7 - - - -
319C ASN* 3.4 15.7 - - - -
320C ARG* 4.8 4.8 + - - +
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Residues in contact with TYR 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C GLY* 1.3 76.0 - - - +
85C PHE* 1.3 69.9 + - - +
86C GLU* 3.6 28.1 + - + -
106C LYS* 3.9 33.8 + - + -
107C THR 3.3 17.5 - - - +
108C PRO* 4.3 1.6 - - + -
109C ILE* 3.5 10.2 - - - +
315C LYS* 3.9 0.8 - - + +
316C LEU* 3.6 0.2 - - - -
317C VAL* 2.9 73.5 + - + +
319C ASN* 3.7 20.0 - - - -
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Residues in contact with PHE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C TYR* 1.3 74.8 - - - +
86C GLU* 1.3 64.4 + - - +
87C VAL* 3.7 17.9 - - + -
99C VAL* 3.5 44.4 - - + -
100C PHE* 3.9 22.9 - + - -
105C LYS 4.9 0.2 - - - -
106C LYS* 3.1 4.2 - - - -
107C THR* 2.7 45.2 + - - +
109C ILE* 3.8 13.5 - - + -
136C PHE* 3.8 15.3 - + + -
279C PHE* 4.1 16.4 - + + -
313C VAL* 4.5 2.9 - - + -
314C GLY* 3.9 9.9 - - - -
315C LYS 3.2 31.2 - - - -
316C LEU* 3.9 15.5 - - + -
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Residues in contact with GLU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C TYR* 3.6 21.1 + - + -
85C PHE* 1.3 78.7 - - - +
87C VAL* 1.3 71.2 + - - +
88C THR* 3.8 8.2 - - + +
104C GLY* 4.0 17.4 - - - +
105C LYS 3.4 2.5 - - - -
106C LYS* 3.3 33.4 - - + -
314C GLY* 3.2 3.5 - - - -
315C LYS* 2.9 40.6 + - + +
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Residues in contact with VAL 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C PHE* 3.7 11.0 - - + -
86C GLU* 1.3 76.7 - - - +
88C THR* 1.3 59.1 + - - +
89C HIS 3.2 26.9 - - - +
90C ASP* 5.3 0.2 - - - -
99C VAL 3.3 26.0 - - - +
100C PHE* 3.9 16.6 - - + +
102C HIS 3.4 28.0 - - - +
103C ILE* 3.8 8.6 - - - +
104C GLY* 2.8 26.7 + - - +
105C LYS* 3.0 16.3 + - + +
313C VAL* 3.9 8.5 - - + +
314C GLY* 4.2 1.1 - - - -
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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