Contacts of the strand formed by residues 100 - 113 (chain A) in PDB entry 1LWT
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 GLU 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A SER* 5.5 1.3 - - - +
94A ARG 3.1 9.2 - - - +
95A THR* 3.0 30.8 + - + +
98A GLY 4.8 2.4 - - - +
99A VAL* 1.3 80.5 - - - +
101A TYR* 1.3 63.3 + - - +
132A ILE* 2.9 55.1 + - + +
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Residues in contact with TYR 101 (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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93A SER* 3.6 10.2 + - - -
94A ARG* 2.8 36.4 + - + +
96A ILE* 3.3 33.0 - - + +
97A LYS* 4.9 1.0 - - - +
99A VAL* 2.8 42.3 - - + +
100A GLU* 1.3 75.5 - - - +
102A PHE* 1.3 70.3 + - - +
129A SER* 4.7 5.2 - - - -
130A TYR* 2.8 16.6 - - - +
131A PRO* 3.3 35.9 - - + -
132A ILE* 3.5 8.6 - - - +
4C A 5.1 2.4 - - - +
5C T 3.9 35.1 - + + +
6C T 6.2 3.1 - - + -
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Residues in contact with PHE 102 (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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91A ARG* 6.3 2.2 - - - -
92A LEU 3.6 4.7 - - - -
93A SER* 4.3 20.6 - - - -
94A ARG 5.8 0.2 - - - -
101A TYR* 1.3 80.7 - - - +
103A GLU* 1.3 61.6 + - - +
104A VAL* 5.2 0.7 - - - -
128A LYS 4.7 0.2 - - - -
129A SER* 2.9 29.3 - - - -
130A TYR* 2.8 39.6 + + + +
132A ILE* 3.6 33.9 - - + -
135A GLY 3.8 1.3 - - - -
136A PRO* 3.1 48.5 - - + -
139A ALA* 4.7 9.4 - - + -
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Residues in contact with GLU 103 (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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91A ARG* 3.6 7.3 - - - +
92A LEU* 2.5 42.1 + - + +
94A ARG* 2.8 46.2 + - + -
102A PHE* 1.3 73.3 - - - +
104A VAL* 1.3 70.1 + - - +
105A ILE* 3.9 21.1 - - + +
127A SER* 2.8 31.3 + - - +
128A LYS 3.7 1.3 - - - +
129A SER* 3.7 22.4 - - - +
139A ALA* 5.2 0.7 - - - +
30B T 5.7 0.2 - - - +
6C T 5.7 2.0 - - - +
7C T 3.4 12.1 - - - +
8C C 5.5 0.3 + - - -
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Residues in contact with VAL 104 (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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89A VAL* 4.4 13.5 - - + -
90A ARG 3.8 3.6 - - - +
91A ARG* 5.4 1.6 - - + -
102A PHE 5.2 0.9 - - - -
103A GLU* 1.3 81.9 - - - +
105A ILE* 1.3 63.6 + - - +
106A THR* 3.5 9.8 + - + +
126A VAL 3.3 8.8 - - - +
127A SER* 3.6 8.6 - - - -
128A LYS* 3.1 27.2 + - + +
129A SER* 5.6 0.2 - - - -
130A TYR* 5.7 3.6 - - + -
139A ALA* 4.2 27.1 - - + -
142A LEU* 4.6 23.1 - - + -
143A VAL* 4.3 21.5 - - + +
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Residues in contact with ILE 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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88A SER 4.0 0.2 - - - +
89A VAL* 3.3 0.5 - - - -
90A ARG* 3.0 64.2 + - + +
92A LEU* 4.0 22.4 - - + -
103A GLU* 3.9 38.1 - - + +
104A VAL* 1.3 72.0 - - - +
106A THR* 1.3 73.3 + - - +
107A PHE* 5.3 4.0 - - + -
125A GLU* 3.8 34.3 - - + +
126A VAL 3.4 6.3 - - - +
127A SER* 4.5 3.8 - - - +
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Residues in contact with THR 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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88A SER 3.3 5.2 - - - +
89A VAL* 3.4 31.9 - - + -
104A VAL* 3.6 13.6 + - + +
105A ILE* 1.3 86.7 - - - +
107A PHE* 1.3 68.2 + - - +
108A GLU* 2.3 30.0 + - - +
125A GLU* 3.3 2.6 - - - -
126A VAL* 2.6 50.1 + - - +
128A LYS* 6.1 0.3 - - - +
146A TYR* 4.4 10.1 - - + -
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Residues in contact with PHE 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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85A THR* 3.9 12.3 - - + -
86A PRO* 3.5 22.4 - - + +
88A SER* 3.0 42.2 + - - +
90A ARG* 6.4 0.7 - - - -
105A ILE* 5.3 3.8 - - + -
106A THR* 1.3 78.8 - - - +
108A GLU* 1.3 66.1 + - - +
123A VAL* 4.4 5.8 - - + -
124A LYS 3.5 2.7 - - - -
125A GLU* 3.9 25.8 - - + -
146A TYR* 3.0 17.9 + - - +
155A PHE* 3.7 12.4 - - + -
170A HIS* 4.2 27.6 - - + -
171A VAL* 4.2 12.6 - - + -
174A ALA* 4.0 23.6 - - + -
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Residues in contact with GLU 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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87A ARG* 5.6 0.2 - - - +
106A THR* 2.3 35.6 + - - +
107A PHE* 1.3 78.6 - - - +
109A MSE 1.3 64.0 + - - +
110A GLY 3.4 0.7 + - - -
123A VAL* 4.4 3.7 - - - +
124A LYS* 2.7 34.6 + - - +
126A VAL* 3.5 30.8 - - + +
146A TYR* 4.4 13.8 - - + -
155A PHE* 4.0 7.2 - - + -
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Residues in contact with MSE 109 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A GLU* 1.3 75.1 - - - +
110A GLY* 1.3 60.8 + - - +
121A GLU* 4.2 25.4 - - + +
122A LEU* 3.1 33.0 - - - +
123A VAL* 3.5 22.9 - - + +
155A PHE* 4.1 26.3 - - + -
157A TRP* 4.1 23.3 - - + -
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Residues in contact with GLY 110 (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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108A GLU 3.4 5.6 + - - -
109A MSE 1.3 78.3 - - - +
111A GLN* 1.3 70.2 - - - +
121A GLU* 3.6 9.9 - - - +
122A LEU* 2.6 26.1 + - - +
124A LYS* 3.9 10.9 - - - +
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Residues in contact with GLN 111 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A GLY* 1.3 80.0 - - - +
112A LYS* 1.3 62.4 + - - +
113A LYS* 5.8 2.4 - - - -
119A ILE* 4.1 25.2 - - + +
120A VAL 3.2 13.7 - - - +
121A GLU* 4.4 21.3 + - + +
122A LEU* 3.8 3.3 - - - +
124A LYS* 3.0 25.0 + - - +
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Residues in contact with LYS 112 (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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111A GLN* 1.3 80.1 - - - +
113A LYS* 1.3 76.1 + - - +
120A VAL* 2.7 43.1 + - + +
122A LEU* 4.0 12.3 - - + -
124A LYS* 3.7 21.3 - - + +
166A LEU* 3.5 43.5 - - + +
8C C 4.7 12.1 + - - -
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Residues in contact with LYS 113 (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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111A GLN* 5.7 2.4 + - - -
112A LYS* 1.3 92.4 + - - +
114A ALA* 1.3 66.8 + - - +
115A PRO* 3.6 4.3 - - - +
117A GLY* 3.4 12.3 - - - +
118A ARG 3.0 20.0 - - - +
119A ILE* 2.4 56.1 - - - +
120A VAL* 5.0 0.2 - - - -
166A LEU* 5.2 0.2 - - - +
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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