Contacts of the strand formed by residues 124 - 132 (chain B) 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 GLY 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B ARG 5.7 1.1 - - - -
101B TRP* 5.1 0.5 - - - -
103B GLY 3.7 0.3 - - - +
104B LYS* 4.0 7.4 - - - -
105B ARG* 3.2 25.1 + - - +
122B ILE 3.5 2.0 + - - -
123B SER* 1.3 76.0 - - - +
125B PRO* 1.3 79.6 - - - +
126B GLY* 3.4 2.6 + - - -
144B THR* 4.6 4.4 - - - +
145B ARG 4.3 3.8 - - - -
73C ASP* 4.1 14.8 - - - -
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Residues in contact with PRO 125 (chain B).
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 3.9 5.6 - - - +
104B LYS* 3.9 12.6 - - + -
124B GLY* 1.3 85.2 - - - +
126B GLY* 1.3 57.9 + - - +
144B THR* 3.2 2.4 - - - -
145B ARG* 3.0 48.2 + - + +
10C GLY 3.9 16.2 - - - +
11C ILE* 4.5 3.8 - - + -
70C GLN* 3.2 43.1 - - + +
71C GLN* 4.1 2.0 - - - -
72C ASN 3.8 19.5 - - - +
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Residues in contact with GLY 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TRP* 3.5 11.9 - - - -
102B ALA* 3.4 1.0 - - - +
103B GLY* 2.9 33.6 + - - -
124B GLY 3.4 0.2 + - - -
125B PRO* 1.3 75.5 - - - +
127B ALA* 1.3 64.1 + - - +
143B ALA 3.1 13.5 - - - -
144B THR* 4.1 1.6 - - - -
10C GLY 4.7 0.6 + - - -
11C ILE* 3.7 18.9 + - - +
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TRP* 3.2 26.2 - - - +
102B ALA* 4.1 2.0 - - + -
126B GLY* 1.3 75.9 - - - +
128B GLY* 1.3 60.6 + - - +
142B ALA* 3.4 3.5 - - - +
143B ALA* 3.0 32.5 + - + +
11C ILE* 4.1 6.2 - - + +
415C ALA* 3.7 30.5 - - + -
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ILE* 3.6 5.2 - - - +
101B TRP* 3.0 45.6 + - - +
127B ALA* 1.3 77.7 - - - +
129B LEU* 1.3 61.9 + - - +
141B LEU 3.2 12.3 - - - -
142B ALA* 4.1 0.9 - - - -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ILE* 4.5 7.4 - - + -
95B LEU* 3.9 17.5 - - + -
98B SER* 3.6 27.1 - - - +
99B THR 3.4 11.0 - - - +
100B ILE* 3.9 18.2 - - + -
101B TRP* 4.3 0.2 - - - +
128B GLY* 1.3 73.4 - - - +
130B GLU* 1.3 59.5 - - - +
132B ILE* 3.7 25.7 - - + +
140B SER* 3.6 2.1 - - - -
141B LEU* 2.9 44.5 + - + +
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B GLN* 5.2 0.5 - - - +
98B SER* 3.2 4.2 - - - -
99B THR* 2.8 54.9 + - - +
101B TRP* 4.0 8.5 - - + +
105B ARG* 2.9 43.1 + - - -
107B TYR* 4.1 7.9 - - - +
108B GLN* 2.8 35.5 + - - +
129B LEU* 1.3 73.9 - - - +
131B ASN* 1.3 83.3 + - - +
132B ILE 3.4 2.0 - - - -
140B SER* 3.6 5.8 - - - +
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Residues in contact with ASN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B PRO 4.6 0.7 - - - +
97B GLY 3.9 14.5 - - - +
98B SER* 3.5 13.9 + - - -
99B THR* 4.9 2.5 - - - +
108B GLN* 4.6 3.3 + - - -
130B GLU* 1.3 93.8 - - + +
132B ILE* 1.3 64.1 + - - +
133B ASP* 3.4 3.5 + - - -
138B LYS* 3.6 43.4 + - + +
139B LEU 3.3 3.3 + - - -
140B SER* 3.0 16.5 + - - -
178B GLN* 5.3 1.6 + - - -
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 3.7 31.0 - - + -
98B SER* 4.2 7.2 - - - -
129B LEU* 3.7 46.4 - - + +
130B GLU 4.7 1.1 - - - -
131B ASN* 1.3 72.8 - - - +
133B ASP* 1.3 70.4 + - - +
134B VAL* 3.3 11.7 + - + -
138B LYS* 3.4 3.3 - - - -
139B LEU* 2.7 64.3 + - + +
141B LEU* 4.4 11.4 - - + -
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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