Contacts of the strand formed by residues 2 - 14 (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 ASP 2 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C VAL* 1.3 77.4 + - - +
3C PHE* 1.3 58.3 + - - +
4C HIS* 4.0 20.2 + - + +
45C LYS 3.5 1.0 - - - +
46C LEU* 3.3 6.6 - - - -
47C GLY 2.7 36.4 + - - +
48C GLN* 4.2 3.3 - - - -
49C GLU* 4.5 1.9 + - - +
59C TYR* 2.6 41.9 + - - +
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Residues in contact with PHE 3 (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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1B VAL* 3.3 42.6 - - + -
46B LEU* 3.7 41.5 - - + -
47B GLY 4.5 3.8 - - - -
48B GLN* 4.3 18.1 + - + +
60B PHE* 4.2 12.8 - + - -
62B THR* 5.0 0.7 - - - -
1C VAL 3.9 1.6 + - - +
2C ASP* 1.3 72.0 - - - +
4C HIS* 1.3 73.5 + - - +
44C LEU* 4.5 17.0 - - + -
45C LYS 3.4 12.1 - - - -
46C LEU* 4.0 13.5 - - + -
421C TRP* 3.2 51.5 - + - +
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Residues in contact with HIS 4 (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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2C ASP* 4.0 27.3 - - + +
3C PHE* 1.3 78.6 + - - +
5C GLY* 1.3 58.3 + - - +
45C LYS* 2.7 51.9 + - + +
47C GLY 6.2 0.2 - - - -
59C TYR* 4.8 4.9 - - - -
61C ASP* 6.2 0.4 - - - -
421C TRP* 2.5 49.3 + - - +
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Residues in contact with GLY 5 (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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4C HIS* 1.3 77.9 - - - +
6C TYR* 1.3 60.7 + - - -
43C GLU* 3.1 13.2 - - - -
45C LYS* 4.2 13.4 - - - +
420C TRP* 3.2 6.6 - - - +
421C TRP* 2.9 40.1 + - - +
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Residues in contact with TYR 6 (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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5C GLY* 1.3 75.7 - - - +
7C ALA* 1.3 78.5 + - - +
8C ARG* 3.0 42.0 + - - +
33C ARG* 3.1 7.5 + - - -
41C TYR* 3.8 24.5 - + - -
42C ALA* 3.3 1.9 - - - +
43C GLU* 2.7 45.8 + - + +
113C HIS* 5.6 0.2 - + - -
418C GLU* 2.6 39.8 + - + -
419C ILE 3.4 12.8 - - - -
420C TRP* 3.9 22.7 - + + -
421C TRP* 3.3 3.7 - - - -
1F GLC 4.9 9.9 - - - -
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Residues in contact with ALA 7 (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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60B PHE* 4.1 17.5 - - + -
84B ALA* 5.1 3.4 - - + -
6C TYR* 1.3 81.2 - - - +
8C ARG* 1.3 62.1 + - - +
41C TYR 3.2 10.3 - - - +
42C ALA* 4.0 12.6 - - + -
417C MET* 3.9 10.7 - - + +
418C GLU* 3.4 4.0 - - - +
419C ILE* 2.8 55.5 + - + +
421C TRP* 3.8 0.6 - - + -
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Residues in contact with ARG 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C TYR* 3.0 36.1 + - - +
7C ALA* 1.3 76.1 - - - +
9C SER* 1.3 64.9 + - - +
33C ARG* 3.4 7.1 - - - +
37C GLU* 3.5 33.0 + - - +
39C GLU* 2.9 44.5 + - - +
40C THR* 3.3 4.2 - - - +
41C TYR* 2.9 45.5 + - - +
116C ASP* 4.3 3.0 + - - -
416C GLN* 3.9 10.3 - - - +
417C MET* 3.4 14.8 - - - +
418C GLU* 4.5 4.0 - - + -
1F GLC 2.8 40.4 + - - -
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Residues in contact with SER 9 (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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84B ALA* 3.4 21.1 - - - -
103B GLY* 3.4 5.2 - - - -
104B LYS* 3.2 25.1 + - - +
8C ARG* 1.3 77.5 - - - +
10C GLY* 1.3 59.2 + - - +
39C GLU 4.7 0.9 - - - -
40C THR* 2.7 26.8 + - - -
70C GLN* 3.6 3.0 + - - +
416C GLN* 3.5 5.7 - - - +
417C MET* 2.8 40.5 + - - +
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Residues in contact with GLY 10 (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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103B GLY* 4.6 7.9 - - - -
125B PRO* 3.9 15.0 - - - +
126B GLY 4.9 3.1 - - - -
9C SER* 1.3 76.9 + - - +
11C ILE* 1.3 63.5 + - - +
20C GLN* 5.9 0.4 - - - -
70C GLN* 3.0 32.1 + - - +
415C ALA 3.3 12.8 - - - -
416C GLN* 3.9 6.8 - - - +
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Residues in contact with ILE 11 (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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125B PRO* 4.1 4.3 - - + +
126B GLY* 3.7 28.5 - - - +
127B ALA* 4.1 12.3 - - + +
143B ALA* 4.0 10.1 - - + +
144B THR 4.0 15.9 - - - +
145B ARG* 3.8 41.5 - - + +
170B ASP* 5.1 0.2 - - - +
10C GLY* 1.3 74.9 - - - +
12C GLY* 1.3 62.3 + - - +
13C TRP* 3.9 32.5 - - + -
20C GLN* 4.4 4.5 - - - +
70C GLN* 5.0 1.3 - - - -
366C PHE* 4.8 0.9 - - - -
414C GLY* 3.3 1.7 - - - -
415C ALA* 2.9 35.7 + - + +
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Residues in contact with GLY 12 (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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145B ARG* 3.0 24.6 + - - +
11C ILE* 1.3 79.2 - - - +
13C TRP* 1.3 65.5 + - - -
20C GLN* 3.1 37.5 + - - +
70C GLN* 5.7 0.4 + - - -
413C PHE 3.3 11.0 - - - -
414C GLY* 4.1 0.4 - - - -
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Residues in contact with TRP 13 (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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143B ALA* 4.2 21.1 - - + -
144B THR 6.0 0.2 - - - -
145B ARG* 3.3 10.2 - - - +
170B ASP* 2.7 34.8 + - + -
172B PHE* 4.3 17.2 - + - -
197B ASN* 3.4 16.8 - - - +
11C ILE* 3.9 37.5 - - + -
12C GLY* 1.3 76.2 - - - -
14C THR* 1.3 62.5 + - - +
18C GLY 3.7 3.1 - - - -
20C GLN* 3.7 6.2 - - - +
412C THR* 3.2 6.9 - - - -
413C PHE* 2.8 76.9 + + + -
414C GLY* 4.1 15.5 - - - -
415C ALA* 6.1 0.7 - - + -
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Residues in contact with THR 14 (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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197B ASN* 5.8 0.3 + - - -
13C TRP* 1.3 77.1 - - - +
15C GLY* 1.3 61.7 + - - +
16C SER* 3.7 8.5 - - - +
17C GLY* 2.9 38.0 + - - +
18C GLY 2.9 8.6 + - - +
19C GLU 2.7 20.7 + - - -
21C GLN* 3.0 33.6 + - - +
410C GLU* 3.4 36.6 - - + +
411C TRP 3.8 3.8 - - - +
412C THR* 3.9 1.8 - - + +
413C PHE* 4.9 1.0 - - - -
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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