Contacts of the strand formed by residues 104 - 109 (chain A) in PDB entry 1L1T
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 SER 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LYS* 3.0 27.0 + - - -
83A VAL* 4.6 5.8 - - - +
84A ALA 3.4 14.4 - - - -
85A SER* 4.6 2.0 - - - +
86A ALA* 4.4 1.5 - - - +
99A CYS* 4.1 0.5 - - - -
100A PHE* 3.0 31.2 + - - -
102A ASP* 2.8 21.9 + - - -
103A GLY* 1.3 80.5 - - - +
105A GLU* 1.3 63.7 + - - +
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Residues in contact with GLU 105 (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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82A ALA 3.8 0.7 - - - +
83A VAL* 3.3 7.4 - - - +
84A ALA 2.9 41.2 + - - +
86A ALA* 3.2 32.1 - - + +
88A GLU 5.0 0.2 - - - +
90A LEU* 3.5 12.4 - - - +
97A VAL* 3.7 20.9 - - + +
98A PHE 3.2 14.6 - - - +
99A CYS* 4.2 11.6 - - - -
100A PHE* 3.9 7.0 - - - -
104A SER* 1.3 78.4 + - - +
106A LEU* 1.3 60.2 + - - +
107A ARG* 2.6 36.3 + - + +
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Residues in contact with LEU 106 (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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14A LEU* 4.0 25.4 - - + -
18A ILE* 4.5 11.4 - - + -
64A PHE* 3.9 27.8 - - + -
71A LEU* 6.1 0.9 - - + -
81A TYR* 3.7 30.5 - - + -
82A ALA 3.6 11.7 - - - +
83A VAL* 4.1 6.3 - - + +
97A VAL* 3.5 2.8 - - - +
98A PHE* 2.9 56.5 + - + -
100A PHE* 3.8 21.4 - - + -
105A GLU* 1.3 71.6 - - - +
107A ARG* 1.3 58.7 + - - +
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Residues in contact with ARG 107 (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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80A ARG 3.7 0.5 - - - +
81A TYR* 3.3 11.6 - - - -
82A ALA* 2.8 42.7 + - + +
84A ALA* 3.7 23.0 - - - +
85A SER 2.7 29.9 + - - -
88A GLU* 3.6 22.2 + - - +
89A PRO 3.9 13.7 + - - -
90A LEU* 3.5 23.2 - - + +
91A GLU* 4.5 12.7 - - - +
94A THR* 4.1 13.5 - - + +
96A VAL 3.8 3.6 - - - -
97A VAL* 4.4 3.8 - - + -
105A GLU* 2.6 33.5 + - + +
106A LEU* 1.3 76.8 - - - +
108A TYR* 1.3 59.9 + - - +
109A ARG* 4.1 7.3 + - + +
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Residues in contact with TYR 108 (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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33A ILE* 4.1 24.0 - - + -
73A SER* 4.7 2.5 - - - -
74A HIS 3.9 1.9 + - - -
75A LEU* 3.9 21.2 - - + -
79A GLY* 3.5 22.0 - - - -
80A ARG 3.5 11.7 - - - -
81A TYR* 3.6 32.3 - + + -
94A THR* 3.5 2.8 - - - +
95A HIS* 3.0 25.8 + - + -
96A VAL* 2.9 24.4 + - + +
98A PHE* 5.3 1.1 - - + -
106A LEU 4.2 0.2 + - - -
107A ARG* 1.3 72.7 - - - +
109A ARG* 1.3 60.6 + - - +
110A ASP* 2.8 40.6 + - + -
115A GLY* 3.5 15.2 - - - -
117A MET* 3.8 23.8 - - + -
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Residues in contact with ARG 109 (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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78A GLU 3.9 1.5 - - - +
79A GLY* 3.3 1.2 - - - -
80A ARG* 2.9 43.1 + - + +
82A ALA* 6.0 6.5 - - - -
91A GLU* 3.4 36.4 + - - +
92A PRO* 3.1 29.5 + - - +
93A HIS* 3.2 13.0 - - + +
94A THR* 3.4 25.1 - - + +
107A ARG* 5.2 6.7 - - + +
108A TYR* 1.3 78.9 - - - +
110A ASP* 1.3 63.6 + - - +
111A VAL* 6.0 2.2 - - + +
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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