Contacts of the strand formed by residues 118 - 124 (chain A) in PDB entry 5AFK
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 SER 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.0 17.0 - - - +
51A VAL* 4.4 1.6 - - - +
52A PHE 3.6 8.2 + - - -
53A TRP* 4.2 9.9 - - - -
99A VAL* 3.6 2.3 - - - +
100A LEU* 2.8 47.6 + - - +
101A THR* 3.0 29.4 + - - -
116A LEU 3.5 1.6 + - - -
117A PRO* 1.3 73.8 - - - +
119A ILE* 1.3 58.2 + - - +
93E ALA 5.4 0.5 + - - -
145E TRP* 4.8 2.5 - - - -
1205E L0B 4.6 6.0 - - - -
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A VAL* 3.3 3.1 - - - +
52A PHE* 2.9 56.9 + - + -
54A LEU* 3.7 32.1 - - + -
97A PRO* 3.8 19.7 - - + -
98A GLU 3.4 6.7 - - - +
99A VAL* 4.5 11.4 - - + -
100A LEU* 4.3 4.9 - - - -
117A PRO* 4.0 21.5 - - + +
118A SER* 1.3 81.8 + - - +
120A ARG* 1.3 73.7 + - - +
121A GLN* 4.3 1.8 - - + +
1206A GOL 3.7 21.5 - - - +
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Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A MET* 3.9 21.5 - - - +
40A ASP* 5.5 2.4 - - - +
49A ASP* 2.7 40.4 + - - +
50A VAL 3.4 7.2 - - - +
51A VAL* 4.0 15.0 - - + +
96A LYS 4.4 0.5 - - - +
98A GLU* 2.9 56.1 + - + +
100A LEU* 4.3 4.8 - - + +
119A ILE* 1.3 74.6 - - - +
121A GLN* 1.3 66.3 + - - +
122A ARG* 6.0 1.6 - - + +
94E ILE* 3.8 41.2 + - - +
95E SER* 5.7 0.2 - - - -
122E ARG* 5.1 9.7 - - - +
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Residues in contact with GLN 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASP* 4.4 1.1 - - - -
50A VAL* 3.0 38.2 + - - +
52A PHE* 3.9 9.1 - - + -
90A ALA* 4.3 1.6 - - - +
93A ALA* 3.4 18.6 - - - +
95A SER* 2.9 32.0 + - - +
97A PRO* 3.4 27.3 - - + +
119A ILE* 4.3 1.6 - - + -
120A ARG* 1.3 78.6 - - - +
122A ARG* 1.3 70.7 + - - +
123A PHE* 3.4 24.9 - - + -
1206A GOL 2.5 28.2 + - - -
100B LEU 5.3 3.0 + - - -
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Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 4.4 11.7 - - + -
48A VAL 3.3 6.5 - - - +
49A ASP* 3.7 35.5 + - + -
93A ALA* 3.6 6.6 - - - +
94A ILE* 2.9 41.4 + - + +
95A SER* 3.1 40.3 + - - +
120A ARG* 5.8 2.1 - - + +
121A GLN* 1.3 74.2 - - - +
123A PHE* 1.3 60.6 + - - +
98B GLU* 5.2 4.6 + - - -
120B ARG* 4.1 16.2 - - - +
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Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 3.2 2.9 - - - -
48A VAL* 2.8 45.0 + - + +
50A VAL* 3.7 27.8 - - + -
52A PHE* 3.9 9.6 - + - -
90A ALA* 3.6 25.8 - - + -
92A ASN* 3.7 27.1 - - - +
93A ALA* 3.8 11.9 - - + -
94A ILE* 4.1 4.7 - - - -
121A GLN* 3.4 39.0 - - + -
122A ARG* 1.3 76.7 - - - +
124A SER* 1.3 67.6 + - - +
140A LEU* 4.1 21.8 - - + -
141A LYS 5.2 0.2 - - - -
142A PHE* 4.2 15.0 - + - -
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Residues in contact with SER 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLN 3.5 6.3 - - - -
47A VAL* 4.4 1.6 - - - +
92A ASN* 3.2 36.4 + - - -
94A ILE* 4.0 12.3 - - - +
123A PHE* 1.3 74.6 - - - +
125A CYS* 1.3 62.3 + - - +
139A LYS 4.7 2.3 + - - +
37B GLN* 2.7 34.3 + - - +
165B ILE* 4.1 5.0 - - - +
167B TYR* 2.8 29.6 + - - -
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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