Contacts of the strand formed by residues 98 - 109 (chain A) in PDB entry 1SEK
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 VAL 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ALA* 4.3 1.6 - - - +
95A VAL* 2.9 58.1 - - + +
96A LYS 3.1 6.5 - - - +
97A GLY* 1.3 86.7 - - - +
99A ASP* 1.3 60.3 + - - +
100A LEU* 4.1 11.7 - - + -
180A PHE* 3.7 20.6 - - + -
181A LYS 3.7 4.5 - - - +
182A GLY* 4.0 1.6 - - - -
234A TYR* 3.8 33.9 - - + -
239A ALA* 4.0 9.9 - - + -
371A LEU* 5.4 0.7 - - + -
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Residues in contact with ASP 99 (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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98A VAL* 1.3 71.9 - - - +
100A LEU* 1.3 59.9 + - - +
101A LYS* 3.2 27.0 + - - -
154A ASN* 4.0 10.0 - - - +
156A ARG* 5.3 1.2 + - - -
179A TYR* 3.4 23.9 + - - +
180A PHE* 3.3 6.9 - - - -
181A LYS* 2.8 41.6 + - + +
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Residues in contact with LEU 100 (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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94A ALA* 4.4 8.5 + - - +
95A VAL* 3.9 25.6 - - + +
98A VAL* 3.7 9.5 + - + -
99A ASP* 1.3 75.0 + - - +
101A LYS* 1.3 64.5 + - - +
102A MET* 4.2 16.0 + - + +
178A ILE* 4.1 23.8 - - + -
179A TYR 3.5 12.3 - - - +
180A PHE* 4.2 15.0 - - + -
371A LEU* 4.2 10.8 - - + -
373A TYR* 5.4 2.2 - - + -
378A MET* 3.7 36.3 - - + -
379A PHE* 4.8 1.3 - - + -
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Residues in contact with LYS 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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99A ASP* 3.2 23.0 + - - +
100A LEU* 1.3 76.6 + - - +
102A MET* 1.3 64.4 + - - +
103A ALA* 4.3 0.4 - - + -
152A GLN 3.5 26.1 + - - +
153A THR* 4.0 10.3 - - + -
154A ASN* 3.0 38.8 - - - +
177A ALA 4.4 0.2 - - - -
178A ILE* 3.1 4.7 - - - +
179A TYR* 2.7 53.6 + - + +
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Residues in contact with MET 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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46A SER* 3.6 7.0 - - - +
48A PHE* 4.0 25.8 - - + -
49A SER* 3.8 20.6 - - - -
100A LEU* 4.2 16.5 + - + -
101A LYS* 1.3 79.6 - - - +
103A ALA* 1.3 59.9 + - - +
177A ALA 3.2 6.3 - - - +
178A ILE* 3.4 30.7 - - + -
378A MET* 3.5 30.7 - - + +
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Residues in contact with ALA 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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101A LYS* 4.3 0.6 - - + -
102A MET* 1.3 75.5 - - - +
104A SER* 1.3 63.0 + - - +
148A TRP* 3.6 23.4 - - + -
152A GLN* 3.7 30.1 - - + +
153A THR* 5.5 2.0 - - + -
175A VAL 4.1 0.2 - - - +
176A ASN* 3.5 5.9 + - - +
177A ALA* 2.7 45.5 + - + +
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Residues in contact with SER 104 (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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49A SER 3.6 4.5 + - - -
52A PRO* 5.8 1.1 - - - -
53A PRO* 2.8 30.6 - - - +
103A ALA* 1.3 71.5 - - - +
105A LYS* 1.3 65.5 + - - +
127A GLY 4.8 2.9 + - - +
128A SER* 3.4 27.9 + - - -
129A GLU* 3.8 10.2 + - - +
148A TRP* 3.7 8.0 - - - -
175A VAL 3.6 6.2 + - - -
176A ASN* 2.9 19.6 + - - +
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Residues in contact with LYS 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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104A SER* 1.3 75.9 - - - +
106A ILE* 1.3 68.7 + - - +
107A TYR* 3.4 27.1 + - + +
128A SER* 3.7 2.4 + - - -
129A GLU* 2.8 57.0 + - + +
131A GLN* 3.6 41.1 + - - +
148A TRP* 3.4 37.8 - - + +
173A VAL 3.9 0.9 - - - +
174A LEU* 3.6 4.9 - - - +
175A VAL* 3.1 33.6 + - - +
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Residues in contact with ILE 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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56A GLN* 3.2 37.2 - - + +
57A LEU* 3.5 33.2 - - + -
105A LYS* 1.3 78.6 - - - +
107A TYR* 1.3 64.4 + - - +
108A VAL* 4.2 18.4 - - + -
118A PHE* 5.7 0.7 - - + -
128A SER* 4.7 0.2 - - - +
129A GLU 2.8 14.7 + - - +
130A VAL* 3.2 13.8 - - + +
131A GLN 2.9 25.1 + - - +
172A SER* 4.8 7.9 - - - +
173A VAL 3.6 9.2 - - - +
174A LEU* 4.1 13.5 - - + -
315A LEU* 4.9 9.4 - - + -
324A VAL* 6.2 2.9 - - + -
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Residues in contact with TYR 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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105A LYS* 3.4 24.9 + - + +
106A ILE* 1.3 77.2 - - - +
108A VAL* 1.3 62.0 + - - +
131A GLN* 3.0 42.6 + - + -
133A VAL* 4.0 18.4 - - + -
135A PHE* 3.7 17.7 - - + -
144A ALA* 4.3 2.9 + - + -
145A ILE* 3.8 45.5 - - + -
148A TRP* 3.3 31.1 - + - +
172A SER* 3.0 5.5 - - - -
173A VAL* 2.8 38.1 + - + +
175A VAL* 4.0 18.6 - - + -
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Residues in contact with VAL 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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106A ILE* 4.2 14.1 - - + -
107A TYR* 1.3 78.8 - - - +
109A ALA* 1.3 68.0 + - - +
112A LEU* 4.5 10.3 - - + +
114A LEU* 3.2 32.8 - - + -
130A VAL* 4.3 12.3 - - + -
131A GLN 2.9 11.4 + - - +
132A ASN* 3.2 12.4 - - - +
133A VAL 3.1 19.4 + - - -
135A PHE* 3.6 4.9 - - - -
171A ARG 3.3 7.9 - - - +
172A SER* 4.0 11.7 - - - -
315A LEU* 4.7 5.4 - - + -
316A LEU* 5.3 0.9 - - + -
322A LEU* 4.6 12.1 - - + -
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Residues in contact with ALA 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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108A VAL* 1.3 71.8 - - - +
110A LYS* 1.3 59.1 + - - +
111A GLY 3.3 4.0 + - - +
112A LEU* 3.3 28.8 + - + +
132A ASN* 2.6 25.1 + - - -
133A VAL 3.6 5.2 - - - -
135A PHE* 3.4 10.8 - - + +
170A THR 3.8 18.6 - - - +
171A ARG* 2.8 11.5 + - - +
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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