Contacts of the strand formed by residues 103 - 112 (chain L) in PDB entry 3IT8
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 103 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98L TYR* 4.0 12.3 - - + +
99L GLU* 3.5 2.8 - - - +
100L THR 3.0 29.6 + - - +
101L GLY 3.7 1.2 - - - +
102L LEU* 1.3 84.2 - - + +
104L PHE* 1.3 62.1 + - - +
213L ILE* 3.5 40.2 - - + -
215L LYS* 4.2 21.1 - - - +
228L TYR* 5.1 3.6 - - + +
284L PHE* 3.5 43.7 - - + -
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Residues in contact with PHE 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I ASN* 3.7 22.2 - - - -
31I ARG* 3.1 51.4 - - + +
32I ARG 4.6 5.8 - - - -
98L TYR* 3.2 25.9 + - - +
99L GLU* 4.1 8.1 - - + -
102L LEU 3.4 9.6 - - - -
103L LEU* 1.3 77.8 - - - +
105L GLY* 1.3 60.2 + - - +
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Residues in contact with GLY 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97L CYS* 3.2 6.1 - - - +
98L TYR* 3.0 49.8 + - - +
104L PHE* 1.3 79.7 - - - +
106L SER* 1.3 60.2 + - - -
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Residues in contact with SER 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96L GLY 3.3 12.3 - - - -
97L CYS* 3.9 9.4 - - - +
98L TYR* 4.1 2.0 - - - -
105L GLY* 1.3 75.9 - - - -
107L TYR* 1.3 65.6 + - - +
159L GLU* 2.6 42.7 + - - +
163L CYS* 5.2 2.9 - - - -
164L SER* 5.9 3.6 - - - -
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Residues in contact with TYR 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L THR* 5.5 2.1 - - - +
3L LEU 3.4 17.8 + - - -
4L LYS* 3.6 17.0 - - - +
94L ILE* 3.8 11.2 - - + -
95L THR* 2.8 29.9 + - - -
96L GLY* 2.8 46.1 + - - +
97L CYS* 3.8 11.0 + - - -
98L TYR* 4.5 4.5 - + + -
106L SER* 1.3 80.4 + - - +
108L GLY* 1.3 59.2 + - - +
109L TYR* 4.1 6.1 - + + -
159L GLU* 3.5 14.3 - - - +
244L GLU* 6.0 0.2 - - - +
246L GLY 3.6 27.1 - - - -
247L GLU* 4.0 28.7 - - + +
248L PRO* 3.3 22.9 - - + +
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Residues in contact with GLY 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L ILE 3.2 8.3 - - - -
95L THR* 3.8 8.7 - - - -
107L TYR* 1.3 78.3 - - - +
109L TYR* 1.3 61.7 + - - +
119L ARG* 3.9 3.0 - - - +
120L TYR* 2.8 34.2 + - - +
155L LEU* 4.1 10.3 - - - -
159L GLU* 3.4 15.2 + - - +
247L GLU* 5.4 0.4 + - - -
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Residues in contact with TYR 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93L LEU* 3.6 5.2 - - - +
94L ILE* 2.7 64.5 + - + +
107L TYR* 4.1 9.0 - + - -
108L GLY* 1.3 77.7 - - - +
110L VAL* 1.3 68.0 + - - +
111L GLU* 3.3 24.8 + - + -
118L ALA 3.2 13.7 - - - +
119L ARG* 3.8 9.2 - - + -
120L TYR 4.4 0.4 - - - +
127L PHE* 4.9 1.3 - - - -
130L MET* 3.6 23.6 - - + -
243L TYR* 3.7 12.9 - + - -
247L GLU* 3.7 36.6 - - + -
248L PRO* 3.4 10.0 - - - +
249L GLY* 3.2 27.2 + - - -
325L NAG 4.4 1.7 - - - +
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Residues in contact with VAL 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91L LEU* 3.5 33.9 - - + -
92L SER 3.2 8.7 - - - +
93L LEU* 3.8 19.7 - - + -
109L TYR* 1.3 76.4 - - - +
111L GLU* 1.3 61.4 + - - +
117L LEU* 2.9 37.2 + - + +
118L ALA 2.7 16.1 + - - +
127L PHE* 4.0 14.8 - - + -
130L MET* 3.2 2.8 - - - +
140L MET* 4.0 21.3 - - + -
141L LEU* 4.2 13.9 - - + -
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Residues in contact with GLU 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91L LEU* 3.5 7.5 - - - +
92L SER* 2.9 45.8 + - - -
94L ILE* 4.0 15.7 - - + -
109L TYR* 3.3 20.1 + - + -
110L VAL* 1.3 74.4 - - - +
112L THR* 1.3 65.9 + - - +
115L GLY 3.9 6.1 - - - +
116L PRO* 3.9 16.2 - - + -
117L LEU* 3.9 1.3 - - - +
243L TYR* 3.1 19.1 + - - -
249L GLY* 5.4 0.9 - - - -
325L NAG 3.7 31.7 + - - +
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Residues in contact with THR 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L LEU* 6.1 0.2 - - - +
80L ILE* 4.7 4.9 - - - +
86L THR* 5.9 1.7 - - + +
88L THR* 3.3 13.6 + - + +
90L SER* 3.8 7.4 + - - -
91L LEU* 3.7 18.1 - - - +
111L GLU* 1.3 78.3 - - - +
113L ALA* 1.3 60.0 + - - +
114L ASN* 2.8 46.0 - - + +
115L GLY* 2.8 30.3 + - - +
117L LEU* 4.1 17.4 - - - +
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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