Contacts of the strand formed by residues 97 - 108 (chain A) in PDB entry 1UHG
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 TYR 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A GLN* 4.0 12.5 + - - +
90A ILE* 3.4 40.7 - - - +
92A LYS 5.1 0.2 - - - -
94A ASN* 2.9 55.9 + - - +
96A VAL* 1.3 90.7 - - + +
98A SER* 1.3 69.3 + - - +
99A PHE* 4.5 1.1 - - + -
180A PHE* 3.9 13.9 - + + -
181A LYS 3.3 13.9 - - - +
182A GLY* 3.7 8.1 - - - -
234A PHE* 6.0 4.5 - - + -
235A ALA 5.0 2.9 - - - -
238A THR* 3.7 23.5 + - + +
239A MET* 3.6 28.2 - - + +
152B GLN* 3.6 9.2 - - - +
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Residues in contact with SER 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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94A ASN* 5.4 0.2 - - - +
97A TYR* 1.3 77.5 - - - +
99A PHE* 1.3 60.5 + - - +
100A SER* 4.2 7.9 + - - -
179A VAL 3.7 1.0 - - - +
180A PHE* 3.3 6.8 - - - -
181A LYS* 2.9 36.5 + - - +
100B SER* 5.7 0.2 + - - -
151B SER 5.1 4.0 - - - -
152B GLN* 4.9 12.9 + - - -
154B ASN* 3.7 28.4 + - - +
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Residues in contact with PHE 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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30A CYS* 4.2 13.0 - - - -
32A ILE* 4.6 2.7 - - + -
33A ALA* 5.2 1.6 - - + -
87A LEU* 4.0 19.7 - - + -
90A ILE* 3.3 55.7 + - + +
91A THR* 3.9 26.0 - - + +
97A TYR* 4.4 5.3 - - + -
98A SER* 1.3 75.1 + - - +
100A SER* 1.3 58.7 + - - +
101A LEU* 3.9 8.5 + - + -
178A ILE* 3.2 30.3 - - + -
179A VAL 3.4 4.5 - - - -
180A PHE* 4.2 11.9 - + + -
239A MET* 5.3 2.9 - - + -
377A LEU* 5.3 2.2 - - + -
378A PHE* 3.6 31.9 - + - -
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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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98A SER* 4.5 8.3 + - - -
99A PHE* 1.3 72.0 - - - +
101A LEU* 1.3 59.5 + - - +
152A GLN 3.9 20.9 + - - -
153A THR* 4.7 5.9 - - - +
154A ASN* 4.2 15.9 + - - -
177A ALA 3.8 0.5 - - - +
178A ILE* 2.8 22.1 - - - +
179A VAL* 2.9 32.3 + - - +
154B ASN* 4.9 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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33A ALA* 3.9 26.7 - - + -
36A SER* 5.2 2.5 - - - +
87A LEU* 3.6 29.8 - - + -
91A THR* 4.4 8.2 - - + +
99A PHE* 3.9 8.3 + - + -
100A SER* 1.3 75.0 - - - +
102A ALA* 1.3 59.4 + - - +
103A SER* 3.8 12.1 + - - -
148A TRP* 5.8 0.2 - - - -
152A GLN* 5.5 5.6 + - - +
176A ASN* 4.0 15.0 - - - +
177A ALA 3.5 16.4 - - - +
178A ILE* 4.1 10.1 - - + -
401A SO4 3.3 36.4 + - - +
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Residues in contact with ALA 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 4.2 0.2 - - - -
101A LEU* 1.3 72.0 - - - +
103A SER* 1.3 59.9 + - - +
148A TRP* 3.8 29.8 - - + -
149A VAL* 4.6 6.6 - - + +
152A GLN* 4.0 21.8 - - + -
153A THR* 4.3 12.8 - - + -
175A VAL* 3.6 3.6 - - - +
176A ASN* 3.5 2.6 + - - -
177A ALA* 2.9 41.0 + - + +
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Residues in contact with SER 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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36A SER* 5.3 2.4 + - - -
37A ALA* 3.7 18.2 + - - +
40A MET* 5.1 5.4 - - - +
101A LEU* 3.8 17.6 + - - +
102A ALA* 1.3 74.1 - - - +
104A ARG* 1.3 65.0 + - - +
127A GLY* 3.4 20.9 + - - -
128A GLY 3.7 2.8 + - - -
148A TRP* 3.8 2.4 - - - -
174A LEU* 4.8 1.4 - - - +
175A VAL 3.2 4.8 + - - -
176A ASN* 2.9 29.7 + - - -
401A SO4 4.3 11.7 + - - -
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Residues in contact with ARG 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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40A MET* 4.3 3.3 - - - +
103A SER* 1.3 79.3 + - - +
105A LEU* 1.3 69.4 + - - +
106A TYR* 3.2 43.2 + - + -
127A GLY 3.2 17.2 + - - -
128A GLY 3.4 13.2 - - - +
130A GLU* 3.9 23.7 + - + +
148A TRP* 3.4 39.0 - - + +
173A VAL 3.5 1.4 - - - +
174A LEU* 3.5 9.1 - - - +
175A VAL* 2.9 39.4 + - + +
95B ASP* 2.7 40.2 + - - +
183B LEU* 5.5 1.2 - - - +
339B ARG* 3.4 14.7 - - - +
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Residues in contact with LEU 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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40A MET* 3.6 24.0 - - + +
41A VAL* 3.8 23.1 - - + -
104A ARG* 1.3 73.7 - - - +
106A TYR* 1.3 59.1 + - - +
117A TYR* 3.8 22.9 - - + +
128A GLY 2.8 9.3 + - - +
129A LEU* 3.0 14.5 - - + +
130A GLU 2.9 25.8 + - - -
172A MET* 3.8 36.1 - - + -
173A VAL 3.3 1.8 - - - +
174A LEU* 4.0 29.4 - - + -
315A ILE* 4.6 6.7 - - + -
323A ILE* 4.8 4.7 - - + -
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Residues in contact with TYR 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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104A ARG* 3.2 43.7 + - + -
105A LEU* 1.3 72.8 - - - +
107A ALA* 1.3 59.4 + - - +
130A GLU* 3.2 30.3 - - + -
132A ILE* 4.0 26.5 - - + -
134A PHE* 3.9 6.4 - - + -
144A LEU* 4.6 2.1 + - + -
145A ILE* 3.7 55.5 - - + -
148A TRP* 3.4 23.9 - + - +
172A MET* 3.0 5.4 - - - +
173A VAL* 2.7 44.8 + - + +
175A VAL* 4.0 16.8 - - + -
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Residues in contact with ALA 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 LEU 3.9 0.8 + - - -
106A TYR* 1.3 74.4 - - - +
108A GLU* 1.3 71.4 + - - +
111A TYR* 5.3 0.7 - - + -
113A ILE* 4.2 17.5 - - + -
129A LEU* 3.7 20.2 - - + -
130A GLU 3.0 7.0 + - - +
131A PRO* 3.4 5.0 - - + +
132A ILE 3.0 19.8 + - - -
134A PHE* 4.1 3.4 - - - -
171A ALA 3.6 4.9 - - - +
172A MET* 3.9 16.6 - - + -
321A LEU* 4.8 6.5 - - + -
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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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107A ALA* 1.3 74.2 - - - +
109A GLU* 1.3 68.6 + - - +
110A ARG* 2.4 45.5 + - - +
111A TYR* 3.1 43.4 + - + +
131A PRO* 5.5 0.2 - - - +
132A ILE 3.3 6.5 - - - -
133A ASN* 3.6 6.2 - - - +
134A PHE* 3.4 22.0 + - + -
135A GLN* 2.9 43.7 + - + +
168A SER 5.9 0.2 - - - +
170A THR 3.7 15.9 - - - +
171A ALA 2.8 17.1 + - - +
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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