Contacts of the strand formed by residues 38 - 46 (chain U) in PDB entry 2FD6
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 LEU 38 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A GLY* 3.9 13.5 - - - +
40A GLN* 3.6 27.1 - - + +
29U VAL 3.7 0.5 - - - +
30U ARG* 3.1 4.2 - - - +
31U LEU* 2.7 60.3 + - + +
37U GLU* 1.3 77.7 - - - +
39U GLU* 1.3 72.2 + - - +
40U LEU* 3.4 25.8 - - + -
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Residues in contact with GLU 39 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LYS* 4.7 12.3 + - - -
28U ILE* 3.6 22.5 - - + +
29U VAL 3.3 4.0 - - - +
30U ARG* 3.6 36.5 + - + -
37U GLU* 4.8 7.9 - - - +
38U LEU* 1.3 81.0 - - - +
40U LEU* 1.3 67.9 + - - +
41U VAL* 3.7 17.9 + - + +
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Residues in contact with LEU 40 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 4.2 10.8 - - + -
29A HIS 4.1 3.8 - - - +
30A TRP* 3.8 19.7 - - + -
40A GLN* 3.6 41.5 - - + +
98A LYS* 6.0 0.7 - - - +
8U THR* 4.2 8.7 - - + -
27U THR 3.8 0.4 - - - +
28U ILE* 3.3 5.9 - - - +
29U VAL* 2.7 56.3 + - + +
31U LEU* 4.4 3.8 - - + -
38U LEU* 3.4 36.3 - - + +
39U GLU* 1.3 80.0 - - - +
41U VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 41 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LYS* 5.9 1.2 - - - +
6U CYS* 5.2 2.7 - - + +
7U LYS 3.4 18.0 - - - +
8U THR* 3.5 14.1 + - - +
26U THR* 4.1 13.9 - - + -
27U THR 3.4 3.8 - - - +
28U ILE* 4.3 8.5 - - + -
39U GLU* 3.7 28.2 + - + +
40U LEU* 1.3 80.5 - - - +
42U GLU* 1.3 65.1 + - - +
43U LYS* 3.7 28.9 - - + -
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Residues in contact with GLU 42 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A SER 4.5 4.9 - - - +
28A ILE* 3.9 38.1 - - + +
29A HIS* 5.5 3.1 + - - -
6U CYS* 3.6 14.8 - - - +
7U LYS* 5.0 2.5 - - - -
8U THR* 4.2 12.8 + - + +
25U ARG* 3.0 36.6 + - - +
26U THR* 4.1 0.2 - - - +
27U THR 2.7 40.1 + - - +
41U VAL* 1.3 76.8 - - - +
43U LYS* 1.3 71.1 + - - +
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Residues in contact with LYS 43 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4U MET* 3.3 11.4 - - + +
5U GLN* 3.3 3.8 - - - +
6U CYS* 3.1 49.5 + - + +
25U ARG* 3.1 10.8 + - - +
26U THR* 3.7 14.8 - - + +
41U VAL* 3.7 21.8 - - + -
42U GLU* 1.3 84.4 - - - +
44U SER* 1.3 66.8 + - - +
77U ASN* 3.0 47.9 + - - +
78U GLN* 3.2 20.0 + - - +
79U GLY 3.5 7.9 + - - -
80U ASN* 4.7 6.1 + - - +
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Residues in contact with SER 44 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3U CYS* 3.9 2.0 - - - -
4U MET 3.1 12.9 + - - -
5U GLN* 4.1 11.7 - - - +
15U GLU* 3.5 12.1 - - - -
25U ARG* 2.8 60.6 + - - +
43U LYS* 1.3 76.9 - - - +
45U CYS* 1.3 70.2 + - - +
77U ASN* 3.1 7.6 + - - -
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Residues in contact with CYS 45 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3U CYS* 3.6 12.1 - - - -
15U GLU* 2.8 40.4 + - - +
17U CYS* 2.0 59.7 - - + -
21U GLN* 4.0 19.1 + - + +
23U LEU 3.4 4.9 - - - -
44U SER* 1.3 87.7 + - - +
46U THR* 1.3 62.0 + - - +
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Residues in contact with THR 46 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A SER* 5.1 1.9 + - - -
21U GLN* 3.1 28.8 - - - +
23U LEU* 2.5 48.5 + - + +
24U CYS 4.0 1.1 - - - +
25U ARG* 3.6 31.5 - - + +
45U CYS* 1.3 78.2 - - - +
47U HIS* 1.3 74.8 + - - +
50U LYS* 3.2 31.3 - - + +
68U GLU* 5.1 0.3 + - - -
70U VAL* 4.4 1.6 - - + -
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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