Contacts of the strand formed by residues 172 - 182 (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 SER 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ILE* 4.8 6.9 - - - +
107A TYR 3.0 13.7 - - - -
108A VAL* 4.0 14.4 - - - -
135A PHE* 4.2 2.2 - - - -
170A THR* 3.7 1.3 - - - -
171A ARG* 1.3 82.3 - - - +
173A VAL* 1.3 64.6 + - - +
312A LEU* 5.4 0.5 - - - +
315A LEU* 6.1 0.4 - - - -
322A LEU* 4.5 9.1 - - - +
323A TYR 3.0 22.5 + - - -
324A VAL* 3.4 15.7 - - - +
325A ASP* 3.0 32.5 + - - +
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Residues in contact with VAL 173 (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 3.9 1.0 - - - +
106A ILE* 3.6 5.1 - - - +
107A TYR* 2.8 32.9 + - + +
135A PHE* 4.3 10.1 - - + -
145A ILE* 4.5 11.9 - - + -
161A VAL* 5.9 3.4 - - + -
166A LEU* 3.9 17.3 - - + -
170A THR* 3.8 18.4 - - + -
172A SER* 1.3 81.1 - - - +
174A LEU* 1.3 63.7 + - - +
175A VAL* 3.7 24.9 - - + -
324A VAL* 4.7 1.6 - - - -
326A ALA* 3.2 29.2 - - + +
328A ILE* 5.7 4.3 - - + +
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Residues in contact with LEU 174 (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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50A VAL* 6.0 3.1 - - + -
53A PRO* 3.9 30.7 - - + -
54A LEU* 5.2 9.0 - - + -
57A LEU* 4.3 22.2 - - + -
105A LYS 3.6 14.6 - - - +
106A ILE* 4.1 15.0 - - + +
173A VAL* 1.3 74.5 - - - +
175A VAL* 1.3 76.2 + - - +
176A ASN* 5.5 1.6 - - + -
292A LEU* 5.0 10.5 - - + -
296A LEU* 5.7 4.5 - - + -
304A LEU* 5.9 1.8 - - + -
305A PHE* 6.2 1.3 - - + -
324A VAL* 4.4 10.2 - - + +
326A ALA 2.8 12.2 + - - +
327A ALA* 3.1 17.4 - - + -
328A ILE 2.8 25.6 + - - -
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A SER* 3.6 3.5 - - - -
105A LYS 3.1 31.2 + - - +
107A TYR* 4.0 13.2 - - + -
145A ILE* 3.7 17.0 - - + -
148A TRP* 3.7 28.0 - - + -
149A VAL* 4.9 0.9 - - + -
160A LEU* 3.5 30.5 - - + -
161A VAL* 5.1 2.0 - - + -
173A VAL* 3.7 20.0 - - + -
174A LEU* 1.3 82.2 - - - +
176A ASN* 1.3 63.6 + - - +
328A ILE* 3.3 6.1 - - + +
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Residues in contact with ASN 176 (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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49A SER* 2.9 31.2 + - - +
50A VAL* 3.7 7.6 - - - +
53A PRO* 4.5 0.6 - - + +
103A ALA 3.5 5.9 - - - +
104A SER* 2.9 22.5 + - - +
160A LEU* 3.6 4.1 - - - +
174A LEU* 5.5 3.1 - - + -
175A VAL* 1.3 76.9 - - - +
177A ALA* 1.3 56.6 + - - +
178A ILE* 4.7 2.6 - - - +
292A LEU* 4.1 9.6 - - + -
328A ILE 2.6 13.0 + - - +
329A GLN* 2.6 48.9 - - + +
330A LYS 2.7 31.5 + - - -
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Residues in contact with ALA 177 (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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49A SER* 5.3 0.2 - - - -
101A LYS 3.9 0.6 - - - +
102A MET* 3.2 3.6 - - - +
103A ALA* 2.7 45.5 + - + +
148A TRP* 5.8 1.3 - - + -
149A VAL* 3.8 30.1 - - + -
153A THR* 4.6 7.6 - - + +
157A ILE* 4.4 8.7 - - + -
160A LEU* 4.1 6.3 - - + -
176A ASN* 1.3 77.8 + - - +
178A ILE* 1.3 62.6 + - - +
330A LYS 3.3 8.3 - - - +
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Residues in contact with ILE 178 (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* 3.7 26.0 - - - -
49A SER* 4.3 7.6 - - - +
100A LEU* 4.1 4.3 - - + -
101A LYS 3.1 9.4 - - - +
102A MET* 3.4 35.7 - - + -
153A THR* 5.9 0.2 - - - -
157A ILE* 3.5 4.7 - - - +
177A ALA* 1.3 78.0 - - - +
179A TYR* 1.3 68.8 + - - +
329A GLN* 4.5 7.6 - - + -
330A LYS 3.0 6.5 + - - +
331A ALA* 3.4 25.3 - - + -
332A PHE 3.1 24.1 + - - +
333A ILE* 4.9 4.0 - - + -
379A PHE* 4.0 24.0 - - + -
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Residues in contact with TYR 179 (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* 3.4 27.7 + - - +
100A LEU* 3.5 4.5 - - - +
101A LYS* 2.7 57.0 + - + +
153A THR* 4.6 6.7 - - + +
156A ARG* 3.3 50.1 + - + +
157A ILE* 4.0 13.0 - - + -
178A ILE* 1.3 75.7 - - - +
180A PHE* 1.3 82.0 + - - +
181A LYS* 3.6 25.9 - - + +
332A PHE* 3.4 34.1 - + + -
334A GLU* 3.8 12.3 + - + -
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Residues in contact with PHE 180 (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* 3.7 21.3 - - + -
99A ASP 3.3 12.3 - - - -
100A LEU* 4.2 11.9 - - + -
178A ILE* 5.4 0.4 - - + -
179A TYR* 1.3 86.0 - - - +
181A LYS* 1.3 63.1 - - - +
182A GLY* 3.6 23.3 - - - -
234A TYR* 3.7 21.1 - + - -
241A MET* 4.6 5.8 - - + -
332A PHE 3.1 6.2 + - - +
333A ILE* 3.7 12.7 - - + -
334A GLU* 2.9 42.2 + - - +
335A VAL* 5.0 1.3 - - + -
371A LEU* 3.5 42.2 - - + -
379A PHE* 3.6 32.1 - + + -
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Residues in contact with LYS 181 (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* 3.7 1.0 - - - +
99A ASP* 2.8 35.7 + - + +
179A TYR* 3.6 23.8 - - + +
180A PHE* 1.3 81.8 - - - +
182A GLY* 1.3 64.0 + - - +
334A GLU* 3.8 34.5 + - + +
336A ASN* 3.5 25.6 - - - +
338A GLU* 2.6 39.1 + - - +
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Residues in contact with GLY 182 (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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97A GLY 3.6 6.7 - - - -
98A VAL* 4.0 2.7 - - - -
180A PHE* 3.6 21.8 - - - -
181A LYS* 1.3 78.6 - - - +
183A SER* 1.3 61.3 + - - -
184A TRP* 5.4 1.2 + - - -
234A TYR* 3.8 13.5 + - - -
334A GLU 4.4 2.2 + - - -
336A ASN* 4.9 2.6 - - - +
338A GLU* 4.1 21.8 - - - +
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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