Contacts of the strand formed by residues 94 - 105 (chain A) in PDB entry 6S1M
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 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A LEU* 4.2 15.9 - - + -
93A PRO* 1.3 76.6 - - - +
95A ILE* 1.3 68.5 + - - +
96A PHE* 4.1 8.3 - - + -
131A THR* 5.0 9.9 - - + -
137A VAL* 4.2 24.7 - - + -
266A LEU 4.4 0.4 - - - -
267A GLU* 3.2 7.8 - - - +
268A LEU* 2.9 62.2 + - + +
273A TYR* 4.0 14.9 + - + -
275A LEU* 5.0 3.1 - - + -
286A LEU* 4.1 24.5 - - + -
288A ALA* 4.5 9.6 - - + -
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Residues in contact with ILE 95 (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 PRO* 4.4 12.5 + - + -
94A LEU* 1.3 83.1 - - - +
96A PHE* 1.3 64.7 + - - +
131A THR* 4.1 14.7 - - - +
132A ASP* 4.2 8.2 + - + +
265A TRP* 4.2 12.7 - - + -
266A LEU 3.5 7.9 - - - +
267A GLU* 4.1 24.0 - - + +
298A HIS* 5.3 2.2 - - + -
304A TRP* 4.2 32.8 - - + -
306A ARG* 6.0 0.2 - - - +
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Residues in contact with PHE 96 (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 LEU* 4.9 11.0 - - + -
95A ILE* 1.3 76.6 - - - +
97A GLN* 1.3 61.1 + - - +
98A GLN* 4.5 9.9 - - + -
127A ALA* 4.4 6.1 - - + -
128A PHE 4.4 4.5 - - - -
129A GLY* 3.7 33.4 - - - -
130A VAL 3.4 17.7 - - - +
131A THR* 4.1 9.0 - - + -
137A VAL* 4.1 24.5 - - + -
139A CYS* 4.1 26.5 - - + -
265A TRP* 3.5 9.7 - - - -
266A LEU* 2.9 64.8 + - + +
268A LEU* 4.8 15.5 - - + -
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Residues in contact with GLN 97 (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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96A PHE* 1.3 73.8 - - - +
98A GLN* 1.3 61.0 + - - +
99A LEU* 4.6 12.3 - - - +
129A GLY* 3.1 3.3 - - - -
130A VAL* 2.9 36.9 + - + +
263A CYS* 3.8 11.5 + - - +
264A ASN 3.2 23.3 - - - +
265A TRP* 3.6 36.9 - - + +
306A ARG 3.8 5.7 + - - -
307A ILE* 4.4 6.5 - - - +
308A ALA* 3.9 20.0 + - + +
310A LEU* 4.7 4.9 - - - +
537A ARG* 3.1 30.5 - - - +
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Residues in contact with GLN 98 (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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96A PHE* 4.1 7.9 + - + -
97A GLN* 1.3 73.4 - - - +
99A LEU* 1.3 70.5 + - - +
100A GLU 4.6 3.2 - - - +
101A ILE* 3.5 26.7 - - - +
127A ALA* 4.8 6.5 - - + +
128A PHE 3.3 12.3 - - - +
129A GLY* 3.9 1.3 - - - -
255A MET* 5.0 5.2 - - - +
260A ILE* 4.5 16.9 - - - +
261A VAL 3.0 28.1 + - - -
262A GLY* 4.9 0.4 - - - -
263A CYS* 3.5 21.0 + - - +
264A ASN* 3.2 24.2 + - - +
266A LEU* 4.2 23.6 - - + +
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Residues in contact with LEU 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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97A GLN* 4.6 13.5 - - - +
98A GLN* 1.3 89.1 - - - +
100A GLU* 1.3 59.6 + - + +
128A PHE* 2.8 13.4 + - + +
129A GLY* 5.0 5.2 - - - -
130A VAL* 5.2 1.1 - - + -
263A CYS* 4.8 17.5 + - - -
310A LEU* 4.3 24.2 - - + -
391A ASP* 3.3 39.3 - - + +
392A VAL* 5.1 4.0 - - + -
423A ARG* 5.9 3.8 - - - +
453A GLY 5.3 4.3 - - - +
455A VAL* 4.7 21.7 - - + +
542A PRO* 5.7 2.1 - - - +
543A LEU* 4.7 26.0 + - + +
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Residues in contact with GLU 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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98A GLN* 4.6 1.3 - - - +
99A LEU* 1.3 79.5 + - + +
101A ILE* 1.3 78.3 + - + +
102A ASP* 5.2 3.3 - - - +
127A ALA* 3.6 2.9 - - - +
128A PHE* 3.0 40.9 + - + +
451A MET 4.3 5.4 - - - +
452A VAL* 3.8 2.6 - - - +
453A GLY* 2.7 44.0 + - - +
454A ARG 3.7 15.7 - - - +
455A VAL* 5.0 7.5 - - + +
544A SER* 5.2 15.3 + - - +
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Residues in contact with ILE 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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98A GLN* 3.5 24.7 - - - +
100A GLU* 1.3 90.6 - - + +
102A ASP* 1.3 67.7 + - - +
125A LEU* 5.9 6.3 - - + -
126A ARG 3.4 11.7 - - - +
127A ALA* 4.8 4.5 - - + -
128A PHE* 4.9 0.7 - - - -
251A GLU* 3.7 28.0 - - + -
254A PHE* 6.3 3.4 - - + -
255A MET* 3.6 34.8 - - + -
260A ILE* 5.8 4.7 - - + -
542A PRO* 4.1 19.3 - - + -
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Residues in contact with ASP 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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100A GLU* 5.2 3.7 - - - +
101A ILE* 1.3 80.9 - - - +
103A HIS* 1.3 71.5 + - - +
125A LEU* 3.5 11.4 - - - +
126A ARG* 2.7 77.3 + - + +
128A PHE* 4.1 9.6 - - + -
251A GLU* 4.2 8.0 + - - -
452A VAL* 4.7 16.5 - - - +
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Residues in contact with HIS 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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102A ASP* 1.3 90.2 + - - +
104A TYR* 1.3 70.4 + - - +
105A VAL* 3.6 17.0 - - + +
123A PRO* 3.7 27.4 - - + +
124A VAL 4.3 2.5 + - - -
125A LEU* 5.1 2.9 - - - +
126A ARG* 4.2 1.7 + - - -
217A PRO* 3.9 15.0 - - + +
218A ARG* 3.3 34.0 + - - -
250A PHE* 3.3 24.8 - + + -
251A GLU* 3.4 22.4 + - - +
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Residues in contact with TYR 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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103A HIS* 1.3 82.4 + - - +
105A VAL* 1.3 77.5 + - - +
106A GLY* 4.5 7.4 - - - -
107A PRO* 4.4 11.1 - - + +
123A PRO* 3.4 2.9 - - - +
124A VAL* 2.7 67.5 + - + +
126A ARG* 3.9 45.5 - - + +
140A HIS* 5.0 10.8 - + - -
278A LYS* 6.1 2.2 - - - -
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Residues in contact with VAL 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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103A HIS* 3.6 26.4 + - + +
104A TYR* 1.3 88.1 - - - +
106A GLY* 1.3 60.3 + - - +
107A PRO* 4.2 3.3 - - - +
122A VAL* 3.7 21.5 - - + -
123A PRO* 4.9 4.9 - - + -
216A LEU* 5.4 14.6 - - + -
217A PRO* 5.9 1.3 - - + -
218A ARG* 4.6 19.5 - - + +
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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