Contacts of the strand formed by residues 61 - 70 (chain C) in PDB entry 4FMF
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 61 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ARG* 4.0 7.2 - - - +
58C PRO 4.5 11.0 - - - +
59C SER 4.3 7.9 - - - +
60C VAL* 1.3 74.4 - - - +
62C ILE* 1.3 66.4 + - - +
63C THR* 3.5 2.8 + - - +
128C THR* 3.3 2.9 - - - -
129C PHE 2.9 37.3 + - - +
85D MET* 3.4 38.7 - - + +
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Residues in contact with ILE 62 (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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101A ARG* 4.1 15.1 - - - +
53C PHE* 4.1 23.6 - - + -
56C PRO* 5.6 3.6 - - + -
60C VAL* 3.8 15.2 + - + +
61C LYS* 1.3 75.5 - - - +
63C THR* 1.3 64.3 + - - +
64C GLN* 3.9 8.7 - - - +
65C VAL* 4.0 16.2 - - + -
83C PRO* 3.9 15.0 - - + +
104C PHE* 3.6 44.7 - - + +
105C THR* 4.9 5.6 - - + -
126C PHE* 4.0 11.9 - - + -
127C ALA 3.8 9.0 - - - +
128C THR* 4.0 15.5 - - + +
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Residues in contact with THR 63 (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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61C LYS* 4.0 7.3 + - - +
62C ILE* 1.3 76.2 - - - +
64C GLN* 1.3 60.4 + - - +
82C ASN* 3.7 8.5 - - - +
83C PRO* 3.4 21.2 - - - +
127C ALA* 2.8 16.4 + - - -
129C PHE* 4.3 3.3 + - - +
63D THR* 2.9 34.3 - - + -
64D GLN* 2.9 22.2 + - - +
82D ASN* 3.5 17.6 + - - +
85D MET* 5.1 4.1 - - - -
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Residues in contact with GLN 64 (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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62C ILE* 3.7 2.7 - - - +
63C THR* 1.3 83.0 - - - +
65C VAL* 1.3 67.1 + - - +
66C THR* 3.4 19.1 + - - +
80C ILE* 3.6 25.5 - - + +
81C TYR 3.8 7.2 - - - +
82C ASN* 3.1 12.3 + - - +
83C PRO* 4.6 0.9 - - - -
125C GLU 3.8 1.0 - - - +
126C PHE* 3.7 1.7 - - - -
127C ALA* 2.8 36.4 + - + +
63D THR* 2.8 33.8 + - + -
127D ALA* 4.0 6.2 - - + +
128D THR 3.2 36.7 + - - +
129D PHE* 4.2 1.0 - - - +
133D ASN* 3.7 6.9 + - - -
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Residues in contact with VAL 65 (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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62C ILE* 4.0 9.6 - - + -
64C GLN* 1.3 75.3 - - - +
66C THR* 1.3 64.7 + - - +
67C TRP* 4.4 0.4 - - + -
79C ALA 4.1 0.2 - - - +
80C ILE* 3.3 3.5 - - - +
81C TYR* 2.7 54.5 + - + +
83C PRO* 5.8 0.4 - - + -
99C PHE* 4.5 7.3 - - + -
103C SER 4.4 9.9 - - - +
104C PHE 4.2 3.8 - - - +
107C GLY* 4.2 21.1 - - - -
124C CYS* 4.3 12.1 - - - -
125C GLU 3.5 6.3 - - - +
126C PHE* 3.4 41.5 - - + -
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Residues in contact with THR 66 (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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64C GLN* 3.4 18.0 + - - +
65C VAL* 1.3 79.2 + - - +
67C TRP* 1.3 75.6 + - - +
68C GLN* 4.0 7.8 + - + +
77C ASN* 4.0 15.9 - - - +
79C ALA 3.6 8.3 - - - +
80C ILE* 4.0 12.5 - - + +
123C ILE 3.5 1.6 - - - +
124C CYS* 3.5 1.4 - - - -
125C GLU* 2.8 46.7 + - - +
127C ALA* 6.2 0.2 - - - +
127D ALA* 5.6 0.2 - - - +
133D ASN* 3.4 31.9 + - - +
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Residues in contact with TRP 67 (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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49C LEU* 3.3 42.6 - - + -
50C HIS 4.1 7.2 - - - -
51C CYS* 3.5 16.8 - - + -
65C VAL* 5.4 0.4 - - + -
66C THR* 1.3 76.5 - - - +
68C GLN* 1.3 58.2 + - - +
77C ASN* 3.7 1.2 - - - -
78C VAL* 2.7 43.3 + - + -
79C ALA* 2.8 18.4 + - + +
99C PHE* 4.0 13.0 - + - -
107C GLY* 2.8 20.8 + - - -
109C ILE* 3.4 33.5 - - + +
122C TYR* 3.6 36.3 - + + -
123C ILE 3.3 16.4 - - - -
124C CYS* 3.6 26.3 - - + -
136C SER* 5.7 0.4 - - - -
138C LEU* 4.2 8.1 - - + -
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Residues in contact with GLN 68 (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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66C THR* 4.1 9.0 - - + +
67C TRP* 1.3 79.0 - - - +
69C LYS* 1.3 61.2 + - - +
70C SER 4.2 0.2 - - - -
75C LYS* 3.6 52.7 + - + +
76C GLN 3.2 11.7 - - - +
77C ASN* 3.4 27.5 + - - +
78C VAL* 3.8 4.7 - - - -
122C TYR* 3.5 5.0 - - - +
123C ILE* 2.7 42.0 + - + +
125C GLU* 4.3 13.5 - - + +
125D GLU* 4.8 1.4 - - - +
133D ASN* 3.9 23.6 + - - +
135D GLU* 4.9 3.3 + - - +
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Residues in contact with LYS 69 (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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68C GLN* 1.3 75.0 - - - +
70C SER* 1.3 64.8 + - - +
71C THR* 3.8 18.3 + - + +
74C SER 3.6 0.7 - - - +
75C LYS* 3.5 2.8 - - - -
76C GLN* 2.8 52.4 + - + +
78C VAL* 3.6 8.8 - - + +
93C TYR* 3.6 12.3 + - - +
117C GLU 2.7 29.7 + - - -
118C ASP* 3.7 5.9 - - - +
119C GLU 2.9 25.0 + - - -
120C GLY* 4.2 2.7 - - - -
121C VAL 3.4 10.5 - - - +
122C TYR* 3.6 33.7 - - + +
123C ILE* 4.5 0.9 - - - -
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Residues in contact with SER 70 (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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69C LYS* 1.3 72.4 - - - +
71C THR* 1.3 58.8 + - - +
72C ASN* 2.9 20.7 + - - -
73C GLY 3.7 9.5 + - - -
74C SER 3.0 12.5 + - - -
75C LYS* 4.4 6.5 - - - +
120C GLY* 4.4 4.0 - - - -
121C VAL* 2.7 38.5 + - - +
123C ILE* 3.6 22.2 - - - +
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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