Contacts of the strand formed by residues 101 - 109 (chain D) in PDB entry 3RT0
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 101 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D TRP* 3.3 5.6 - - - -
94D ILE* 3.7 19.8 - - + +
95D LEU* 3.7 2.8 - - - -
96D ASP* 2.8 45.7 + - + +
99D GLU* 3.8 24.2 - - + +
100D HIS* 1.3 81.0 - - - +
102D LEU* 1.3 62.3 + - - +
119D THR* 3.9 21.3 - - + -
120D ILE 3.3 11.2 - - - +
121D SER* 3.9 15.0 - - - -
123D HIS* 6.3 0.7 - - + -
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Residues in contact with LEU 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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43D TRP* 4.0 10.3 - - + -
46D VAL* 3.2 30.3 - - + +
47D ARG* 4.5 11.7 - - - +
49D PHE* 4.7 7.2 - - + -
55D TYR* 5.5 3.8 - - - +
75D ARG* 6.0 0.9 - - - +
92D LEU* 3.5 28.3 - - + -
94D ILE 3.4 2.9 - - - +
95D LEU* 4.2 17.7 - - + -
101D ILE* 1.3 76.3 - - - +
103D GLY* 1.3 59.4 + - - +
104D ILE* 3.7 23.4 + - + +
118D SER 4.1 0.3 - - - +
119D THR* 3.4 2.1 - - - -
120D ILE* 2.9 48.7 + - + +
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Residues in contact with GLY 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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92D LEU* 3.6 4.5 - - - +
93D GLU* 2.7 34.7 + - - -
94D ILE* 2.7 38.3 + - - +
102D LEU* 1.3 74.5 - - - +
104D ILE* 1.3 57.4 + - - -
118D SER 3.4 9.4 - - - -
119D THR* 4.4 3.4 - - - -
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Residues in contact with ILE 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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49D PHE* 3.6 33.7 - - + -
75D ARG* 4.5 12.3 - - - +
90D GLU* 4.0 21.1 - - + +
91D VAL 3.4 5.8 - - - +
92D LEU* 4.4 0.7 - - - -
93D GLU* 4.1 4.0 - - - +
102D LEU* 3.7 36.5 + - + -
103D GLY* 1.3 76.0 - - - +
105D ARG* 1.3 75.8 + - - +
106D ILE* 4.4 3.4 - - + +
116D TYR* 5.7 2.7 - - + -
117D SER* 3.3 5.4 - - - -
118D SER* 3.0 42.5 + - - +
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Residues in contact with ARG 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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90D GLU* 3.2 2.6 - - - -
91D VAL* 2.8 43.8 + - + +
93D GLU* 3.0 37.3 + - - +
104D ILE* 1.3 80.3 - - - +
106D ILE* 1.3 72.2 + - - +
107D VAL* 4.0 14.1 - - + -
115D ASN* 3.9 38.6 + - - +
116D TYR 3.5 8.3 - - - +
117D SER* 3.7 21.6 + - - +
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Residues in contact with ILE 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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88D SER* 3.8 5.4 - - - +
89D THR 3.5 6.1 - - - +
90D GLU* 3.8 26.0 - - + +
104D ILE* 5.0 2.7 - - + -
105D ARG* 1.3 79.4 - - - +
107D VAL* 1.3 64.0 + - - +
108D GLY 3.6 8.3 - - - +
111D HIS* 2.9 49.6 - - + +
113D LEU* 4.4 14.1 - - + +
115D ASN* 4.8 5.7 + - - -
116D TYR* 3.0 56.1 + - + +
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Residues in contact with VAL 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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74D VAL* 5.4 3.4 - - + -
89D THR* 2.7 39.0 + - + +
90D GLU* 4.3 7.4 - - - +
91D VAL* 3.9 26.5 - - + +
105D ARG* 4.0 13.9 - - + +
106D ILE* 1.3 78.3 - - - +
108D GLY* 1.3 54.7 + - - +
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Residues in contact with GLY 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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89D THR* 2.9 31.5 + - - -
106D ILE* 3.6 4.2 - - - +
107D VAL* 1.3 79.6 - - - +
109D GLY* 1.3 60.2 + - - -
111D HIS* 3.0 18.4 + - - -
114D LYS* 6.2 1.3 - - - -
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Residues in contact with GLY 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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76D GLU* 5.7 0.2 - - - -
87D LYS* 3.4 27.4 - - - -
88D SER* 4.0 0.9 - - - -
89D THR* 4.3 2.9 + - - -
108D GLY* 1.3 75.3 - - - -
110D ASP* 1.3 59.7 + - - -
111D HIS* 3.4 11.0 + - - +
114D LYS* 4.7 9.9 + - - -
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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