Contacts of the strand formed by residues 99 - 109 (chain D) in PDB entry 3F5O
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 ASP 99 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D GLU* 6.3 1.8 - - + -
42D MET 3.6 4.0 - - - +
43D LYS* 3.2 44.7 + - - +
97D GLY 3.8 0.7 + - - +
98D GLU* 1.3 80.9 - - - +
100D ILE* 1.3 62.7 + - - +
122D ASN* 3.8 1.6 - - - +
123D LYS* 2.9 44.0 + - + +
124D ALA 4.7 0.2 + - - -
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Residues in contact with ILE 100 (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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41D GLU* 3.2 8.2 - - - +
42D MET* 2.8 58.3 + - + +
44D VAL* 3.9 20.2 - - + -
55D LEU* 4.0 23.1 - - + -
63D LEU* 4.1 7.0 - - + -
94D ALA* 4.2 4.5 - - + -
98D GLU* 4.1 4.7 - - + +
99D ASP* 1.3 80.1 - - - +
101D VAL* 1.3 65.4 + - - +
102D ILE* 3.9 21.1 - - + -
120D LEU* 4.2 10.3 - - + -
121D THR 3.3 9.4 - - - +
123D LYS* 4.2 0.6 - - - +
129D ILE* 3.5 24.5 - - + -
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Residues in contact with VAL 101 (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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39D ILE* 3.7 27.1 - - + -
40D CYS 3.5 4.5 - - - +
41D GLU* 4.0 13.0 - - + +
100D ILE* 1.3 77.3 - - - +
102D ILE* 1.3 63.4 + - - +
103D THR* 3.7 11.7 - - - +
119D ASP 3.5 1.2 - - - +
120D LEU* 3.2 5.7 - - - +
121D THR* 2.8 46.0 + - - +
123D LYS* 3.7 36.1 - - + +
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Residues in contact with ILE 102 (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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28D ILE* 5.1 0.7 - - + -
38D VAL 3.6 1.9 - - - +
39D ILE* 3.4 2.6 - - - -
40D CYS* 2.8 56.7 + - + +
41D GLU 4.2 0.4 - - - -
42D MET* 4.1 12.8 - - + +
63D LEU* 4.0 27.4 - - + +
67D ILE* 3.7 28.5 - - + +
100D ILE* 3.9 27.6 - - + -
101D VAL* 1.3 74.6 - - - +
103D THR* 1.3 59.9 + - - +
118D VAL* 3.4 27.6 - - + -
119D ASP 3.5 1.8 - - - -
120D LEU* 4.0 19.5 - - + -
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Residues in contact with THR 103 (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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37D LYS* 3.8 29.2 - - - +
38D VAL 3.5 2.7 - - - +
39D ILE* 4.0 13.4 - - + +
101D VAL* 3.7 17.5 - - - +
102D ILE* 1.3 74.1 + - - +
104D ALA* 1.3 62.3 + - - +
105D HIS* 3.8 17.8 + - + -
117D SER 3.9 0.7 - - - +
118D VAL* 3.3 5.0 - - - -
119D ASP* 2.9 45.0 + - - +
121D THR* 5.4 1.6 + - - -
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Residues in contact with ALA 104 (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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37D LYS* 3.3 9.5 - - - +
38D VAL 2.8 31.8 + - - +
67D ILE* 3.5 42.4 - - + +
68D SER* 3.8 11.0 - - - +
71D ALA* 4.1 6.0 - - + +
102D ILE 4.1 0.6 + - - -
103D THR* 1.3 75.0 - - - +
105D HIS* 1.3 60.9 + - - +
117D SER 3.3 4.9 - - - -
118D VAL* 3.9 8.5 - - + -
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Residues in contact with HIS 105 (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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36D GLY 3.3 5.8 - - - -
37D LYS* 3.4 34.1 + - + +
71D ALA* 4.8 0.4 - - - -
103D THR* 3.8 27.1 + - + +
104D ALA* 1.3 74.7 - - - +
106D VAL* 1.3 64.8 + - - +
107D LEU* 3.5 6.9 + - + -
116D THR* 2.7 24.6 + - - -
117D SER* 2.9 34.4 + - - +
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Residues in contact with VAL 106 (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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36D GLY* 2.8 27.0 + - - +
71D ALA* 3.7 35.0 - - + +
72D LEU* 3.8 22.4 - - + +
75D THR* 4.1 2.9 - - + -
105D HIS* 1.3 75.1 - - - +
107D LEU* 1.3 62.5 + - - +
108D LYS 4.0 6.5 - - - +
109D GLN* 3.5 35.9 - - + +
115D PHE 3.7 10.3 - - - +
116D THR* 4.2 3.6 - - - +
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Residues in contact with LEU 107 (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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91A MET* 3.5 25.8 - - + -
128A LEU* 3.9 30.7 - - + +
131A GLN* 3.7 26.2 - - - +
105D HIS* 4.5 8.1 - - + +
106D VAL* 1.3 77.7 - - - +
108D LYS* 1.3 59.6 + - + +
115D PHE* 2.7 21.2 + - + +
116D THR 4.3 5.4 - - - +
117D SER* 3.6 30.3 - - - +
133D ARG* 4.3 5.6 - - - -
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Residues in contact with LYS 108 (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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91A MET* 3.2 38.6 - - + +
92A SER* 4.8 8.7 - - - -
127A LYS* 5.9 4.9 - - + +
128A LEU* 5.7 2.5 - - + +
150B COA 3.2 29.4 + - - -
106D VAL* 3.6 1.8 - - - +
107D LEU* 1.3 81.8 - - - +
109D GLN* 1.3 82.3 + - - +
110D GLY* 3.4 8.7 - - - +
114D ALA* 3.4 2.8 - - - +
115D PHE* 2.8 51.2 + - + +
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Residues in contact with GLN 109 (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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36D GLY* 5.8 0.6 - - - -
72D LEU* 4.8 6.3 - - + +
75D THR* 3.4 43.3 + - - +
76D GLU 5.2 0.6 + - - +
77D ARG* 4.7 11.4 + - - +
106D VAL* 3.5 22.1 - - + +
108D LYS* 1.3 85.2 + - - +
110D GLY* 1.3 62.1 + - - +
113D LEU 3.9 2.9 - - - -
114D ALA* 4.4 6.3 - - + +
138D LEU* 5.5 5.0 - - + +
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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