Contacts of the strand formed by residues 47 - 59 (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 VAL 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A VAL* 3.7 1.7 - - - -
42A ASP* 2.9 43.6 + - + +
45A ASN* 3.4 19.5 - - + +
46A GLN* 1.3 80.7 - - - +
48A VAL* 1.3 71.9 + - - +
49A ASP* 5.5 1.3 - - + -
94A ILE* 4.4 8.1 - - + -
122A ARG* 4.4 20.4 - - + -
123A PHE 3.2 14.6 - - - +
124A SER* 5.1 0.7 - - - -
125A CYS* 4.2 1.1 - - - +
127A VAL* 4.0 7.1 - - - +
37B GLN* 4.9 0.4 - - - +
39B MET* 3.5 25.8 - - + -
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Residues in contact with VAL 48 (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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38A ILE* 3.8 21.8 - - + -
40A ASP 3.6 11.0 - - - +
41A VAL* 4.2 2.2 - - + -
47A VAL* 1.3 78.4 - - - +
49A ASP* 1.3 61.4 + - - +
50A VAL* 4.0 17.0 - - + -
121A GLN 4.0 0.7 - - - +
122A ARG* 3.3 2.8 - - - +
123A PHE* 2.8 51.6 + - + +
125A CYS* 4.1 2.9 - - + +
127A VAL* 4.5 2.9 - - + -
138A CYS* 3.7 29.6 - - + -
140A LEU* 5.0 2.0 - - + -
200A PHE* 4.1 18.6 - - + -
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Residues in contact with ASP 49 (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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38A ILE* 3.6 1.7 - - - +
39A MET* 2.7 35.5 + - - +
40A ASP* 2.9 29.8 + - + +
47A VAL* 5.5 1.8 - - + -
48A VAL* 1.3 72.2 - - - +
50A VAL* 1.3 59.2 + - - +
120A ARG* 2.7 51.6 + - - +
121A GLN 3.7 5.1 - - - +
122A ARG* 3.7 28.0 + - + +
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Residues in contact with VAL 50 (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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35A LEU* 4.0 20.0 - - + -
37A GLN 3.4 4.5 - - - +
38A ILE* 4.3 11.4 - - + -
39A MET 4.4 0.2 - - - +
48A VAL* 4.0 24.2 - - + -
49A ASP* 1.3 80.8 + - - +
51A VAL* 1.3 63.7 + - - +
52A PHE* 3.7 13.6 - - + -
119A ILE 3.9 0.5 - - - +
120A ARG* 3.4 2.8 - - - +
121A GLN 3.0 39.0 + - - +
123A PHE* 3.7 24.9 - - + -
140A LEU* 4.6 11.7 - - + -
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Residues in contact with VAL 51 (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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35A LEU* 3.7 3.1 - - - +
36A LEU* 2.9 42.0 + - + -
37A GLN* 2.8 22.2 + - + +
39A MET* 3.6 30.7 - - + -
50A VAL* 1.3 74.2 - - - +
52A PHE* 1.3 65.5 + - - +
100A LEU* 4.1 17.0 - - + -
118A SER* 4.4 2.5 - - - +
119A ILE 3.3 9.4 - - - +
120A ARG* 4.0 19.1 - - + -
93E ALA 5.2 1.3 - - - +
94E ILE* 4.4 16.8 - - + -
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Residues in contact with PHE 52 (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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33A LEU* 3.8 27.4 - - + -
34A SER 3.3 13.2 - - - +
35A LEU* 4.2 4.3 - - + -
36A LEU* 4.1 8.3 - - - +
50A VAL* 3.7 20.6 - - + -
51A VAL* 1.3 76.4 - - - +
53A TRP* 1.3 59.9 + - - +
54A LEU* 3.6 41.0 + - + -
118A SER* 3.6 1.6 + - - -
119A ILE* 2.9 61.5 + - + +
121A GLN* 3.9 19.7 - - + -
123A PHE* 3.9 27.8 - + - -
140A LEU* 5.3 1.1 - - + -
142A PHE* 4.2 7.9 - + - -
1206A GOL 4.4 1.8 - - - -
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Residues in contact with TRP 53 (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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32A SER 3.7 0.5 - - - +
33A LEU* 3.4 2.9 - - - -
34A SER* 2.7 54.0 + - - +
36A LEU* 4.2 9.1 - - + +
52A PHE* 1.3 73.4 - - - +
54A LEU* 1.3 63.2 + - - +
55A GLN* 3.2 38.0 + - + +
116A LEU* 2.9 46.1 + - + +
117A PRO 3.3 20.0 - - - -
118A SER* 4.1 3.8 - - - +
160A ASP* 5.2 3.6 - - - -
145E TRP* 3.8 6.0 - + - -
185E GLU* 5.4 8.1 - - - -
1205E L0B 3.2 69.5 - + + -
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Residues in contact with LEU 54 (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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31A PHE* 3.6 34.1 - - + -
32A SER 3.4 7.9 - - - +
33A LEU* 4.0 11.0 - - + -
52A PHE* 3.6 29.1 + - + -
53A TRP* 1.3 73.3 - - - +
55A GLN* 1.3 63.2 + - - +
56A MET* 4.1 13.0 - - + -
116A LEU* 3.2 26.2 - - - -
117A PRO* 3.0 22.0 + - + +
119A ILE* 3.7 22.4 - - + -
142A PHE* 4.8 1.1 - - + -
1206A GOL 3.9 27.8 - - - +
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Residues in contact with GLN 55 (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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30A TYR 3.4 1.7 - - - +
31A PHE* 3.3 6.6 - - - -
32A SER* 2.8 55.9 + - - +
34A SER* 4.2 8.4 + - - +
53A TRP* 3.2 41.0 - - + +
54A LEU* 1.3 79.2 - - - +
56A MET* 1.3 59.8 + - - +
57A SER* 5.7 0.2 - - - -
116A LEU* 3.7 13.9 - - + +
157A GLN* 4.8 10.2 + - - +
160A ASP* 4.5 4.5 - - - +
1205E L0B 4.2 21.8 - - - -
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Residues in contact with MET 56 (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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29A VAL* 3.8 21.3 - - + -
30A TYR 3.3 2.2 - - - -
31A PHE* 4.0 14.1 - - + -
54A LEU* 4.0 29.1 - - + -
55A GLN* 1.3 73.8 - - - +
57A SER* 1.3 62.2 + - - +
58A TRP* 3.8 12.6 - - + -
85A VAL* 6.2 0.7 - - - -
86A PRO* 4.3 22.7 - - - +
88A LEU* 3.7 21.5 - - - -
114A GLN* 3.7 0.3 - - - -
115A TYR* 2.9 59.7 + - + +
116A LEU* 4.0 2.4 - - - +
117A PRO* 4.7 1.6 - - + -
1206A GOL 4.2 10.8 - - - +
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Residues in contact with SER 57 (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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29A VAL* 3.4 1.2 - - - -
30A TYR* 2.8 55.1 + - - +
55A GLN 5.7 0.2 - - - -
56A MET* 1.3 76.0 - - - +
58A TRP* 1.3 64.4 + - - +
112A HIS* 3.5 19.4 + - - -
113A VAL 3.1 13.2 - - - -
114A GLN* 3.9 11.9 - - - -
116A LEU* 6.1 0.9 - - - -
157A GLN* 5.2 2.6 + - - -
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Residues in contact with TRP 58 (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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20A PRO* 5.1 0.9 - - + -
27A VAL* 4.0 5.4 - - + -
28A THR 3.6 17.3 - - - +
29A VAL* 3.9 11.4 - - + -
30A TYR* 5.2 0.7 - - - -
56A MET* 3.8 22.9 - - + -
57A SER* 1.3 85.4 - - - +
59A THR* 1.3 73.2 + - - +
60A ASP* 4.1 8.0 + - + +
83A LEU* 5.0 2.5 - - + -
84A TRP* 3.3 45.8 + + - -
85A VAL* 3.9 14.8 - - + -
86A PRO* 3.5 31.4 - - + -
105A ALA* 5.6 0.2 - - + -
112A HIS* 3.5 8.2 + - - -
113A VAL* 2.7 68.4 + - + +
115A TYR* 4.2 15.5 - + + -
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Residues in contact with THR 59 (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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20A PRO* 4.4 5.5 - - - +
27A VAL* 4.3 14.0 - - - +
28A THR 4.4 4.0 + - - -
58A TRP* 1.3 78.1 - - - +
60A ASP* 1.3 66.1 + - - +
61A HIS* 3.9 8.5 + - + +
64A GLN* 5.6 0.7 - - - +
110A SER* 3.9 21.7 - - - +
111A GLY 3.6 3.1 - - - +
112A HIS* 3.1 23.0 + - - +
2F NAG 4.8 6.6 + - - -
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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