Contacts of the strand formed by residues 41 - 52 (chain A) in PDB entry 1FNA
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 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLU* 3.0 27.7 + - - +
39A THR 3.2 1.6 + - - -
40A GLY* 1.3 84.8 + - - +
42A ASN* 1.3 63.4 - - - +
43A SER* 3.6 4.9 - - - +
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Residues in contact with ASN 42 (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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41A GLY* 1.3 75.0 - - - +
43A SER* 1.3 72.2 + - - +
44A PRO* 4.1 1.6 - - - +
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Residues in contact with SER 43 (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 GLU* 6.0 8.1 - - - -
41A GLY* 3.6 3.2 - - - +
42A ASN* 1.3 86.6 + - - +
44A PRO* 1.3 80.9 - - - +
45A VAL* 3.6 4.5 + - - +
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Residues in contact with PRO 44 (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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37A GLY* 5.5 1.7 - - - -
42A ASN 4.5 2.7 - - - +
43A SER* 1.3 97.0 - - - +
45A VAL* 1.3 69.8 + - - +
46A GLN* 3.8 15.5 + - - +
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Residues in contact with VAL 45 (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 THR* 3.4 26.7 - - + +
36A TYR 3.4 16.8 - - - +
37A GLY* 4.7 9.2 - - - +
43A SER 4.9 3.6 - - - +
44A PRO* 1.3 82.4 - - - +
46A GLN* 1.3 79.1 + - - +
47A GLU* 4.3 1.4 + - - +
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Residues in contact with GLN 46 (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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34A ILE 3.9 0.2 - - - +
35A THR* 3.2 5.0 - - - -
36A TYR* 2.8 73.6 + - + +
37A GLY* 6.0 0.2 - - - -
44A PRO* 3.9 20.0 + - - +
45A VAL* 1.3 78.8 + - - +
47A GLU* 1.4 65.1 + - - +
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Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ARG* 2.9 53.1 + - + +
34A ILE 3.3 13.0 - - - +
35A THR* 4.0 13.4 - - + +
45A VAL 4.3 1.5 + - - +
46A GLN* 1.4 80.9 + - - +
48A PHE* 1.3 75.6 - - - +
49A THR* 5.2 2.9 + - - -
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Residues in contact with PHE 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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33A ARG* 3.8 3.1 - - - -
34A ILE* 2.9 70.3 + - + +
36A TYR* 3.7 31.2 - + - -
47A GLU* 1.3 79.8 - - - +
49A THR* 1.3 71.6 + - - +
50A VAL* 3.5 9.6 - - + -
57A ALA* 4.0 5.2 - - + -
58A THR 3.8 14.1 - - - -
59A ILE* 3.8 26.5 - - + -
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Residues in contact with THR 49 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A TYR* 3.7 34.2 - - + -
32A TYR 3.3 12.7 + - - +
33A ARG* 4.8 1.0 - - - +
47A GLU* 5.2 4.0 + - - -
48A PHE* 1.3 81.7 - - - +
50A VAL* 1.3 71.8 + - - +
51A PRO* 4.3 5.0 - - + +
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A TRP* 4.0 18.8 - - + -
31A TYR* 3.4 2.4 - - - +
32A TYR* 2.8 39.5 + - + +
34A ILE* 3.3 33.9 - - + -
48A PHE* 3.5 11.9 - - + -
49A THR* 1.3 81.1 - - - +
51A PRO* 1.3 83.6 - - + +
54A LYS* 3.9 17.7 - - + -
56A THR 4.0 5.4 - - - +
57A ALA* 3.8 7.9 - - + -
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Residues in contact with PRO 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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30A ARG 4.5 3.1 - - - +
31A TYR* 4.7 2.2 - - + -
32A TYR* 3.8 1.0 - - - -
49A THR* 4.3 5.6 - - + +
50A VAL* 1.3 100.3 - - + +
52A GLY* 1.3 58.9 + - - +
53A SER* 3.0 21.5 + - - +
54A LYS* 3.1 26.8 + - + +
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Residues in contact with GLY 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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29A VAL* 3.5 34.6 + - - +
30A ARG 3.1 16.4 + - - -
31A TYR* 4.1 0.4 - - - -
32A TYR* 3.7 23.4 + - - -
50A VAL 3.6 1.0 + - - -
51A PRO* 1.3 68.8 - - - +
53A SER* 1.3 58.9 + - - +
54A LYS 3.3 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