Contacts of the strand formed by residues 74 - 79 (chain D) in PDB entry 1XFB
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 ILE 74 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D LYS* 3.7 12.5 + - - -
29D GLY 3.5 2.7 - - - +
31D LEU* 4.5 17.3 - - + +
70D VAL* 2.9 39.4 + - + +
71D LYS 4.1 0.2 - - - +
72D LYS 3.8 0.6 - - - -
73D CYS* 1.3 87.1 - - - +
75D GLY* 1.3 58.7 + - - +
76D GLY 3.5 23.1 - - - +
77D VAL* 4.1 8.3 - - + -
103D ILE* 3.6 34.6 - - + +
300D PHE* 4.2 18.4 - - + -
306D LEU* 4.7 2.7 - - + -
328D PHE* 4.7 4.3 - - + -
332D ALA* 4.0 19.5 - - + -
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Residues in contact with GLY 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ARG 4.3 2.5 - - - +
23D ILE* 3.6 28.2 - - - -
28D LYS* 3.8 21.0 - - - +
29D GLY 2.7 12.3 + - - -
74D ILE* 1.3 73.7 - - - +
76D GLY* 1.3 55.1 + - - -
102D GLY 4.9 0.3 - - - +
103D ILE* 3.6 4.0 - - - +
104D VAL* 2.9 30.8 + - - +
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Residues in contact with GLY 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ILE* 4.4 8.0 - - - +
29D GLY 3.4 3.8 + - - -
30D ILE* 3.3 9.4 - - - -
31D LEU 2.9 24.3 + - - -
74D ILE* 3.4 6.6 - - - +
75D GLY* 1.3 79.9 - - - +
77D VAL* 1.3 63.5 + - - -
103D ILE* 3.5 3.1 - - - +
104D VAL* 3.2 15.7 - - - -
145D PHE* 4.3 7.4 - - - -
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Residues in contact with VAL 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 3.3 23.6 - - + +
33D ALA* 4.8 0.7 - - + -
64D PHE* 3.6 30.7 - - + -
74D ILE* 4.1 8.5 - - + -
76D GLY* 1.3 78.4 - - - +
78D ILE* 1.3 68.7 + - - +
79D PHE* 3.5 20.3 - - + -
98D ILE* 3.9 16.6 - - + -
103D ILE* 3.6 19.7 - - + -
104D VAL 2.9 8.3 + - - +
106D GLY 2.9 23.7 + - - -
145D PHE* 3.9 1.7 - - - -
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Residues in contact with ILE 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 3.6 26.9 - - + -
31D LEU 2.8 11.4 + - - +
32D ALA* 4.1 9.6 - - + -
33D ALA* 3.0 30.7 + - - +
34D ASP* 3.6 23.1 - - + +
77D VAL* 1.3 71.2 - - - +
79D PHE* 1.3 63.3 + - - +
106D GLY 3.5 4.5 - - - -
107D ILE 4.3 3.1 - - - +
108D LYS 4.1 11.4 - - - +
145D PHE* 3.6 14.8 - - + -
147D LYS* 4.0 28.3 - - + +
186D ILE* 4.1 13.5 - - + -
230D LYS* 4.1 3.6 - - - +
301D SER* 3.7 13.9 - - - +
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Residues in contact with PHE 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ALA* 4.3 2.9 - - - -
34D ASP* 3.7 4.9 - - - +
64D PHE* 3.7 28.5 - + - -
77D VAL* 3.5 28.3 - - + -
78D ILE* 1.3 75.3 - - - +
80D PHE* 1.3 64.8 + - - +
83D THR* 3.5 22.2 - - + -
84D LEU* 3.7 24.0 - - + -
94D PHE* 3.8 18.8 - - + -
95D VAL* 4.2 12.1 - - + -
98D ILE* 4.1 19.5 - - + -
105D VAL* 3.6 24.2 - - + -
106D GLY 2.6 19.2 + - - +
107D ILE* 3.4 4.0 - - + -
108D LYS 3.2 24.1 + - - -
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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