Contacts of the strand formed by residues 99 - 105 (chain C) in PDB entry 1AF6
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 THR 99 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C GLN* 3.9 26.0 - - + +
88C GLY 3.3 8.1 - - - +
89C LYS* 3.6 25.4 - - - +
97C GLY 4.0 3.3 + - - -
98C SER* 1.3 74.3 - - - +
100C ILE* 1.3 78.3 - - - +
101C TRP* 4.2 2.8 - - + -
128C GLY 3.8 0.5 - - - +
129C LEU* 3.4 4.5 - - - -
130C GLU* 2.8 61.5 + - - +
131C ASN* 5.7 1.6 - - - +
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Residues in contact with ILE 100 (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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351A TRP* 3.8 44.4 - - + -
363A ILE* 3.6 27.6 - - + +
87C GLN* 3.5 0.3 - - - -
88C GLY 2.7 47.9 + - - +
91C LEU* 3.8 16.2 - - + -
92C ILE* 3.6 27.8 - - + -
98C SER 4.3 0.4 + - - +
99C THR* 1.3 75.8 - - - +
101C TRP* 1.3 62.0 + - - +
128C GLY 3.5 7.0 - - - +
129C LEU* 3.9 13.9 - - + -
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Residues in contact with TRP 101 (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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363A ILE* 4.3 7.4 - - - +
85C ASN* 4.9 1.3 - - + +
86C VAL 3.2 13.9 - - - +
87C GLN* 3.9 15.0 - - + -
99C THR* 4.2 7.0 - - + -
100C ILE* 1.3 79.5 - - - +
102C ALA* 1.3 73.4 + - - +
103C GLY 3.6 10.8 - - - -
105C ARG* 3.2 46.5 - - + +
107C TYR* 3.5 35.0 + + + -
124C GLY 5.1 1.3 - - - -
126C GLY* 3.5 22.2 - - - -
127C ALA* 3.2 24.5 - - - +
128C GLY* 3.0 51.1 + - - +
129C LEU 4.3 0.6 - - - +
130C GLU* 4.1 9.1 + - + +
141C LEU 4.9 0.6 + - - -
142C ALA* 4.0 7.2 - - + -
144C THR* 4.5 11.4 - - + -
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Residues in contact with ALA 102 (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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10A GLY* 5.2 0.2 - - - -
363A ILE* 4.4 10.7 - - + +
415A ALA* 4.5 2.7 - - + +
416A GLN* 4.0 34.1 - - - +
417A MET* 3.4 9.5 - - + +
85C ASN* 3.3 4.8 - - - -
86C VAL 3.2 27.1 + - - +
101C TRP* 1.3 80.8 - - - +
103C GLY* 1.3 60.2 + - - +
126C GLY 3.3 11.0 - - - +
127C ALA* 4.0 8.5 - - + -
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Residues in contact with GLY 103 (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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9A SER* 3.4 23.8 + - - -
10A GLY* 4.4 2.4 - - - -
84C ALA 3.2 11.7 - - - -
85C ASN* 3.8 1.8 - - - -
101C TRP* 3.6 6.8 - - - -
102C ALA* 1.3 75.9 - - - +
104C LYS* 1.3 65.1 + - - -
105C ARG 3.5 1.7 + - - -
125C PRO* 4.4 0.7 - - - -
126C GLY 2.9 29.0 + - - +
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Residues in contact with LYS 104 (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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9A SER* 3.2 14.8 + - - +
40A THR* 3.9 17.3 - - + +
68A VAL* 4.4 3.8 - - - -
70A GLN* 4.3 7.9 - - + -
72A ASN 2.8 24.7 + - - -
73A ASP* 2.9 19.4 + - - +
75A GLU* 2.9 19.4 + - - +
81C PHE* 3.0 28.3 + - - -
82C ARG 3.4 14.3 + - - +
83C GLU* 3.4 4.0 - - - -
84C ALA 2.8 33.1 + - - +
85C ASN* 3.1 12.1 + - - +
103C GLY* 1.3 70.4 - - - -
105C ARG* 1.3 57.5 + - - +
124C GLY 3.5 9.0 - - - +
125C PRO* 4.0 15.0 - - + -
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Residues in contact with ARG 105 (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 ARG 4.4 2.1 + - - -
83C GLU* 3.7 7.9 - - - +
85C ASN* 3.6 22.9 - - - +
87C GLN* 3.9 21.9 + - - +
101C TRP* 3.2 63.7 - - + +
104C LYS* 1.3 76.9 - - - +
106C PHE* 1.3 80.6 + - - +
107C TYR* 3.2 19.0 + - - +
108C GLN* 5.0 4.4 - - - +
123C SER* 3.5 1.2 - - - -
124C GLY 3.1 27.9 + - - +
130C GLU* 2.8 40.8 + - - -
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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