Contacts of the strand formed by residues 63 - 72 (chain A) in PDB entry 3FEO
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 PHE 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLU* 4.5 3.4 - - + -
51A VAL* 3.3 29.4 - - - +
52A PRO* 3.4 19.7 - - + -
53A ASN* 3.9 2.0 - - - +
61A LYS* 4.1 30.7 - - + -
62A VAL* 1.3 82.1 - - - +
64A TRP* 1.3 58.2 + - - +
99A ASP* 4.4 4.9 - - + -
101A HIS* 3.9 13.9 - + - -
105A TRP* 3.4 37.9 - + - -
106A CYS* 3.6 25.4 - - - -
111A LYS* 4.2 14.8 - - + -
112A PRO* 3.5 6.5 + - + +
113A LEU* 3.1 9.9 - - + -
114A VAL 2.7 34.2 + - - -
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Residues in contact with TRP 64 (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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50A GLU* 3.6 5.7 - - - +
51A VAL* 3.1 30.2 + - - +
53A ASN* 4.2 8.9 - - + +
63A PHE* 1.3 73.1 - - - +
65A ILE* 1.3 86.3 + - - +
80A TYR* 3.7 22.9 - - + -
81A GLU* 2.7 24.8 + - + +
113A LEU* 3.9 20.0 - - + -
114A VAL 3.3 27.8 - - - +
115A PRO* 3.8 17.5 - - + -
116A PRO* 3.5 20.3 - - + +
126A TRP* 3.7 38.8 - + + -
129A PHE* 3.9 13.7 - + - -
130A LEU* 3.6 35.9 - - + -
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Residues in contact with ILE 65 (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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48A ARG* 3.8 23.3 - - + -
49A VAL 3.5 7.6 - - - +
50A GLU* 4.0 31.2 - - + +
64A TRP* 1.3 86.8 - - + +
66A ALA* 1.3 58.3 + - - +
80A TYR* 3.2 7.3 - - - +
81A GLU* 2.7 53.4 + - + +
103A VAL* 4.4 5.2 - - + -
113A LEU* 4.4 11.4 - - + -
130A LEU* 4.2 16.2 - - + -
134A LEU* 3.9 37.0 - - + -
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Residues in contact with ALA 66 (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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48A ARG* 3.1 8.2 - - - -
49A VAL* 2.9 40.2 + - + +
51A VAL* 3.8 23.3 - - + -
64A TRP 4.2 0.6 + - - -
65A ILE* 1.3 76.3 - - - +
67A GLY* 1.3 59.0 + - - +
78A LEU* 3.8 22.0 - - + -
79A ARG 3.3 13.5 - - - +
80A TYR* 4.2 4.7 - - + +
81A GLU* 4.2 0.9 - - - +
91A PHE* 4.6 0.7 - - + -
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Residues in contact with GLY 67 (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 ASN* 5.1 3.6 - - - -
47A VAL 3.5 7.4 - - - -
48A ARG* 3.9 11.8 - - - +
66A ALA* 1.3 74.5 - - - +
68A ILE* 1.3 64.0 + - - -
69A VAL* 3.3 3.7 + - - +
78A LEU* 3.4 3.9 - - - -
79A ARG* 3.0 34.5 + - - +
81A GLU* 4.9 3.0 + - - +
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Residues in contact with ILE 68 (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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43A ILE* 4.5 10.8 - - + -
44A SER 3.7 18.8 - - - +
45A GLU* 3.5 18.7 - - - +
46A ASN* 2.9 31.4 + - - +
47A VAL* 3.0 33.2 + - + +
49A VAL* 5.4 1.6 - - + -
67A GLY* 1.3 67.7 - - - -
69A VAL* 1.3 61.4 + - - +
70A LYS 3.9 23.8 - - - +
71A LEU* 4.4 8.1 - - + -
76A ALA* 4.1 5.8 - - + -
77A LEU 3.7 4.3 - - - -
78A LEU* 3.7 20.4 - - + -
95A ILE* 3.8 23.6 - - + -
140A LEU* 6.1 0.2 - - + -
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Residues in contact with VAL 69 (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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45A GLU* 4.5 9.4 - - - +
46A ASN* 5.5 1.1 - - - -
67A GLY 4.1 1.6 - - - +
68A ILE* 1.3 75.0 - - - +
70A LYS* 1.3 60.1 + - + +
77A LEU* 2.8 35.0 + - + +
78A LEU 4.5 0.4 - - - -
79A ARG* 3.7 57.2 - - + +
90A ASP* 4.2 3.4 - - - +
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Residues in contact with LYS 70 (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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18A ILE* 4.4 15.6 + - + -
19A ASN* 3.0 37.6 - - - +
22A SER* 4.7 14.3 + - - +
23A PHE 5.0 5.2 - - - -
45A GLU* 5.7 0.9 - - - -
68A ILE* 3.5 5.5 - - - +
69A VAL* 1.3 84.6 - - + +
71A LEU* 1.3 65.5 + - - +
72A ALA* 6.0 0.7 - - + -
75A ASN 3.9 0.3 - - - +
76A ALA* 3.3 4.0 - - - -
77A LEU* 2.7 51.7 + - + -
92A TRP* 4.1 10.7 - - + -
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Residues in contact with LEU 71 (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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25A ALA* 5.0 4.3 + - - +
27A PRO* 6.1 4.9 - - + -
40A TRP* 3.9 22.9 - - + +
43A ILE* 3.8 37.5 - - + +
44A SER* 4.6 4.0 - - - +
45A GLU* 4.9 7.1 - - + +
68A ILE* 4.4 12.5 - - + +
70A LYS* 1.3 79.1 - - - +
72A ALA* 1.3 61.3 + - - +
73A GLY 3.7 15.5 - - - +
74A TYR 4.7 2.5 - - - +
75A ASN 3.3 19.7 - - - +
76A ALA* 4.2 11.9 - - + -
95A ILE* 5.3 1.6 - - + -
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Residues in contact with ALA 72 (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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18A ILE* 3.9 28.5 - - + -
25A ALA* 3.5 23.3 - - + +
70A LYS* 4.2 1.1 - - + -
71A LEU* 1.3 74.7 - - - +
73A GLY* 1.3 65.9 + - - +
74A TYR 3.1 0.3 + - - -
75A ASN* 2.7 33.0 + - + +
92A TRP* 4.5 13.7 - - + -
418A VAL* 3.7 7.3 - - + +
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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