Contacts of the strand formed by residues 92 - 103 (chain A) in PDB entry 1MUH
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 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ALA* 3.7 22.7 - - + +
89A PHE* 3.6 38.4 - - + +
91A GLU* 1.3 77.2 - - - +
93A LEU* 1.3 70.4 + - - +
131A LEU* 4.4 13.7 - - + -
132A LEU 3.2 17.5 - - - +
133A GLU* 3.8 8.3 - - + -
134A ALA 4.0 0.2 - - - +
140A VAL* 4.3 7.0 - - + -
176A MET* 3.8 27.4 - - + -
179A MET* 4.8 2.9 - - - -
182A ASN* 2.7 18.4 + - + +
183A VAL* 4.3 12.3 - - + -
184A ILE* 2.9 26.9 + - - +
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Residues in contact with LEU 93 (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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92A LEU* 1.3 78.8 - - - +
94A ALA* 1.3 61.3 + - - +
95A ILE* 3.5 14.3 + - + -
130A LEU 3.5 1.9 - - - +
131A LEU* 3.3 6.7 - - - +
132A LEU* 2.7 46.3 + - + +
134A ALA* 3.5 25.6 - - + -
137A PHE* 3.6 33.2 - - + -
184A ILE* 3.3 25.8 - - + +
186A VAL* 4.5 1.1 - - + -
318A ILE* 4.2 27.1 - - + +
321A HIS* 4.2 16.4 - - + -
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Residues in contact with ALA 94 (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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92A LEU 3.9 0.4 + - - -
93A LEU* 1.3 74.6 - - - +
95A ILE* 1.3 66.8 + - - +
96A GLU* 3.7 4.6 + - - +
129A VAL* 3.8 15.0 - - + -
130A LEU 3.7 0.9 - - - -
131A LEU* 3.6 19.5 - - + -
143A LEU* 5.2 2.7 - - + -
172A SER* 5.7 2.5 - - - +
183A VAL* 3.6 19.1 - - + -
184A ILE 2.5 12.6 + - - +
185A ALA* 3.4 9.9 - - + +
186A VAL 3.0 19.9 + - - -
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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 LEU* 3.9 18.4 - - + -
94A ALA* 1.3 69.0 - - - +
96A GLU* 1.3 71.5 + - - +
128A SER 3.3 0.3 - - - +
129A VAL* 2.9 6.9 - - - +
130A LEU* 2.6 49.6 + - + +
132A LEU* 4.4 13.9 - - + -
186A VAL* 3.5 31.2 - - + +
321A HIS* 4.0 21.5 - - + +
322A ARG* 3.4 43.3 - - + +
324A ARG* 5.2 3.4 - - + -
325A ILE* 3.8 19.7 - - + +
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Residues in contact with GLU 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 ALA* 4.3 5.5 - - - +
95A ILE* 1.3 86.3 - - - +
97A ASP* 1.3 65.8 + - - +
127A HIS* 2.7 34.3 + - + +
128A SER 3.2 9.0 - - - +
129A VAL* 4.1 10.1 - - + +
165A TRP* 3.1 37.0 - - + +
168A ALA* 3.2 23.5 - - - +
169A ALA* 5.3 1.0 + - - -
185A ALA* 4.9 4.5 - - - +
186A VAL 3.2 16.1 + - - +
187A CYS* 4.1 11.1 - - - +
188A ASP* 4.8 1.7 + - - +
196A TYR* 4.1 11.9 + - - -
322A ARG* 4.8 2.4 + - - -
325A ILE* 4.2 1.1 - - - -
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Residues in contact with ASP 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 GLU* 1.3 77.6 - - - +
98A THR* 1.3 78.5 + - - +
126A VAL 3.9 0.5 - - - +
127A HIS* 3.3 12.6 - - - -
128A SER* 2.6 39.8 + - - +
165A TRP* 4.6 3.9 - - - -
188A ASP* 3.4 20.4 - - - +
322A ARG* 3.4 5.8 + - - +
325A ILE* 3.7 18.4 - - + +
326A GLU* 3.2 5.5 - - - +
329A HIS* 3.6 11.4 + - + -
478A MN 2.1 36.4 + - - -
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Residues in contact with THR 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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97A ASP* 1.3 92.4 + - - +
99A THR* 1.3 73.7 + - - +
125A TRP* 3.9 16.2 - - + -
126A VAL 3.2 8.5 - - - +
127A HIS* 2.4 28.3 + - - +
148A TRP* 3.9 18.4 - - + -
164A LYS* 2.5 26.8 + - - +
329A HIS* 3.9 5.0 - - - -
478A MN 4.2 2.6 + - - -
20B G 4.1 4.5 + - - +
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Residues in contact with THR 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 THR* 1.3 74.8 - - - +
100A SER* 1.3 74.2 + - - +
101A LEU* 4.8 0.2 - - + -
125A TRP* 3.4 15.0 - - - -
126A VAL* 2.9 34.7 + - + +
128A SER* 5.9 0.2 - - - +
329A HIS* 3.6 27.2 + - + +
332A TRP* 4.1 24.5 - - + -
333A LYS* 2.9 17.7 + - - +
20B G 2.4 28.6 + - - -
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Residues in contact with SER 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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99A THR* 1.3 80.6 + - - +
101A LEU* 1.3 65.0 + - - +
102A SER* 3.9 6.9 - - - -
114A LEU* 3.7 15.2 - - - +
124A TRP 3.3 11.9 - - - -
125A TRP* 3.6 20.7 - - - -
333A LYS* 2.7 33.4 + - - -
339A GLU* 3.5 1.9 + - - +
20B G 5.3 0.7 + - - -
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Residues in contact with LEU 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 THR* 4.8 0.2 - - + -
100A SER* 1.3 81.5 - - - +
102A SER* 1.3 59.5 + - - +
103A TYR* 3.8 19.0 - - + +
114A LEU* 4.0 0.5 - - - +
123A GLY* 3.2 8.1 - - - -
124A TRP* 2.9 38.8 + - + +
126A VAL* 3.6 27.8 - - + -
147A TRP* 3.6 31.0 - - + -
332A TRP* 3.9 26.2 - - + -
333A LYS* 4.1 13.0 - - + -
338A ALA* 4.3 18.6 - - + -
339A GLU* 3.6 3.8 - - + +
353A VAL* 4.0 6.5 - - + -
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Residues in contact with SER 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 SER* 4.8 8.1 - - - -
101A LEU* 1.3 70.9 - - - +
103A TYR* 1.3 73.7 + - - +
104A ARG* 5.3 0.8 - - - +
114A LEU* 3.8 12.5 - - - +
121A SER* 3.6 25.5 + - - -
122A ARG 3.6 3.6 - - - -
339A GLU* 2.9 32.2 + - - +
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Residues in contact with TYR 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 LEU* 3.8 35.6 - - + +
102A SER* 1.3 75.5 + - - +
104A ARG* 1.3 65.2 + - - +
105A HIS* 3.6 30.5 - + + +
107A VAL* 4.9 0.2 - - + -
108A ALA* 3.1 10.5 - - + +
111A LEU* 3.9 22.4 - - + -
121A SER* 3.3 2.5 - - - -
122A ARG 2.7 35.3 + - - +
124A TRP* 4.0 12.9 - + - -
338A ALA 2.7 31.3 + - - -
339A GLU* 3.8 16.3 - - + -
341A GLN 3.6 14.8 - - - -
342A ARG* 4.3 2.5 - - - +
349A LEU* 4.1 15.2 - - + +
353A VAL* 3.5 16.5 - - - +
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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