Contacts of the strand formed by residues 101 - 120 (chain A) in PDB entry 5U2H
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 101 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A PRO 4.8 0.2 - - - +
97A LEU* 3.1 12.1 - - - +
98A GLN* 2.8 45.9 + - - +
99A GLY 3.5 6.1 + - - -
100A ASN* 1.3 79.2 - - - +
102A PHE* 1.3 58.7 + - - +
316A ARG* 6.4 0.2 - - - -
317A PHE 3.0 17.9 - - - -
318A ASP* 3.2 24.2 + - - +
319A ILE* 4.3 1.3 - - - +
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Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 3.6 38.8 - - + +
65A VAL* 4.7 9.6 - - + -
94A THR* 5.0 2.2 - - - +
95A PHE 4.8 8.3 - - - +
96A PRO 5.4 1.1 - - - -
97A LEU* 3.9 15.3 - - + +
101A SER* 1.3 74.6 - - - +
103A PHE* 1.3 59.2 + - - +
104A VAL* 3.9 21.5 - - + -
190A VAL* 3.7 31.2 - - + -
192A ILE* 6.1 0.2 - - + -
231A LEU* 5.6 2.5 - - + -
254A ILE* 5.2 5.4 - - + -
316A ARG* 3.5 2.8 - - - +
317A PHE* 2.7 79.8 + + + +
319A ILE* 4.1 13.5 - - + -
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Residues in contact with PHE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TYR 4.6 4.0 - - - -
94A THR* 3.1 26.0 + - - -
95A PHE* 4.0 30.2 + + + +
102A PHE* 1.3 73.5 - - - +
104A VAL* 1.3 68.8 + - - +
105A MET* 3.6 20.9 - - + -
291A TYR* 3.6 33.2 - + + -
293A PHE* 4.1 17.5 - + + -
312A VAL* 3.7 27.4 - - + -
314A GLY* 3.4 38.4 - - - -
315A ILE 3.7 10.5 - - - -
316A ARG* 4.0 6.3 - - + +
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 4.9 10.8 - - + -
93A TYR* 3.6 22.2 - - + +
94A THR* 4.7 5.2 - - - +
102A PHE* 3.9 26.2 - - + -
103A PHE* 1.3 83.9 - - - +
105A MET* 1.3 74.3 + - - +
106A THR* 3.7 3.6 - - + +
185A ALA* 5.1 3.4 - - + -
188A PHE* 4.8 8.3 - - + -
231A LEU* 4.7 17.5 - - + -
314A GLY* 3.3 0.7 - - - -
315A ILE* 2.8 41.1 + - + +
317A PHE* 4.5 9.9 - - + -
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Residues in contact with MET 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 5.4 3.8 - - - -
92A ASP 4.7 11.4 - - - +
93A TYR* 3.0 25.6 + - + +
103A PHE* 3.6 17.0 - - + -
104A VAL* 1.3 84.2 - - - +
106A THR* 1.3 65.7 + - - +
107A ASN 3.7 13.5 - - - +
108A PHE* 3.7 33.0 - - + -
182A LEU* 2.9 28.3 - - + +
185A ALA* 4.5 2.6 - - - +
188A PHE* 5.7 0.3 - - - -
310A ILE* 5.5 2.2 - - + -
312A VAL* 3.5 32.3 - - + -
313A PHE 3.9 1.6 - - - +
314A GLY* 4.0 0.2 - - - -
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Residues in contact with THR 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 VAL* 3.7 13.2 - - + +
105A MET* 1.3 79.5 - - - +
107A ASN* 1.3 64.0 + - - +
180A ALA* 3.8 4.7 - - - +
181A LEU 3.8 2.9 + - - -
182A LEU* 3.2 34.4 + - - +
185A ALA* 4.9 9.4 - - + -
242A PHE* 4.9 1.8 - - + -
246A ALA* 2.5 43.8 + - + +
249A GLY* 4.5 1.4 - - - -
313A PHE 3.0 10.8 + - - -
314A GLY* 3.7 4.2 - - - -
315A ILE* 3.7 30.3 - - + +
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Residues in contact with ASN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A MET* 3.7 6.0 - - - +
106A THR* 1.3 79.2 - - - +
108A PHE* 1.3 88.8 + - - +
177A PRO* 2.9 55.5 + - - +
180A ALA* 3.9 7.1 - - - +
181A LEU* 3.7 12.8 - - - +
246A ALA 3.4 11.9 - - - +
247A ILE* 3.4 25.1 + - - +
313A PHE* 2.7 35.1 + - + +
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Residues in contact with PHE 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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71A VAL* 5.2 0.9 - - + -
84A VAL* 4.8 17.5 - - + -
88A PHE* 3.6 37.7 - + - -
105A MET* 3.7 27.6 - - + -
107A ASN* 1.3 94.2 + - - +
109A ILE* 1.3 73.1 + - - +
110A LYS* 4.3 18.2 - - + -
177A PRO* 4.7 2.1 - - - +
181A LEU* 3.4 37.1 - - + +
182A LEU* 4.5 1.1 - - + -
310A ILE* 4.5 14.6 - - + -
311A LYS 3.3 11.7 - - - +
312A VAL* 4.6 0.4 - - - -
313A PHE* 4.0 1.8 - - - -
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Residues in contact with ILE 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 PHE* 1.3 80.4 - - - +
110A LYS* 1.3 69.0 + - - +
111A THR* 4.1 7.1 + - - +
171A GLU* 5.4 5.5 - - + +
172A GLU* 5.5 8.1 - - + +
174A LYS* 3.4 50.5 - - + +
175A ASP 4.1 11.7 - - - +
176A ALA* 4.8 0.2 - - - -
177A PRO* 4.7 8.3 - - + -
309A LEU 4.3 0.5 - - - +
310A ILE* 3.5 4.4 - - - +
311A LYS* 2.9 47.9 + - + +
313A PHE* 3.7 22.7 - - + -
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Residues in contact with LYS 110 (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 PHE* 4.2 18.8 - - + -
109A ILE* 1.3 77.6 - - - +
111A THR* 1.3 66.8 + - - +
112A GLU* 4.3 15.3 - - + +
308A THR* 6.0 0.2 - - + -
309A LEU 4.3 1.3 - - - -
310A ILE* 4.4 14.6 - - + -
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 4.7 7.6 + - - +
110A LYS* 1.3 77.6 + - - +
112A GLU* 1.3 67.5 + - - +
114A GLN* 4.3 23.6 + - + +
169A PRO* 4.6 6.7 - - + +
170A ILE 5.3 0.2 - - - -
171A GLU* 3.7 37.1 + - + +
172A GLU* 5.2 1.2 + - - +
307A ARG 4.9 0.3 - - - +
308A THR* 3.1 5.2 - - - +
309A LEU* 3.0 42.0 + - - +
310A ILE* 4.7 1.0 - - - +
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Residues in contact with GLU 112 (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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110A LYS* 4.3 11.4 - - + +
111A THR* 1.3 85.8 - - - +
113A GLY* 1.3 64.0 + - - +
114A GLN 3.4 3.6 + - - -
169A PRO* 5.2 6.1 - - - +
299A TYR* 5.0 2.7 - - - +
308A THR* 3.9 18.8 - - + +
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Residues in contact with GLY 113 (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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112A GLU* 1.3 75.3 - - - +
114A GLN* 1.3 65.2 + - - +
115A GLN* 3.4 11.6 + - - +
168A CYS 3.8 4.8 - - - +
169A PRO* 4.6 5.2 - - - +
299A TYR* 3.7 21.4 + - - -
306A LYS* 5.2 3.8 - - - +
307A ARG 4.1 0.6 + - - -
308A THR* 4.0 4.2 + - - -
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Residues in contact with GLN 114 (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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111A THR* 4.3 14.8 - - + +
112A GLU 3.4 1.8 + - - -
113A GLY* 1.3 78.6 - - - +
115A GLN* 1.3 59.3 + - - +
167A TRP* 3.5 36.9 + - + +
168A CYS 3.3 8.5 - - - +
169A PRO* 2.9 31.1 + - + +
170A ILE* 3.8 1.4 - - - +
171A GLU* 3.7 15.8 - - - +
306A LYS* 3.6 1.7 - - - -
307A ARG* 2.8 43.5 + - - +
309A LEU* 3.3 41.6 + - + +
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Residues in contact with GLN 115 (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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113A GLY 4.3 6.9 - - - +
114A GLN* 1.3 75.6 - - - +
116A GLN* 1.3 76.7 + - - +
117A GLY 3.4 0.2 + - - -
167A TRP* 3.9 7.9 - - - -
168A CYS* 2.9 35.1 + - + +
304A VAL* 4.1 21.9 - - - +
305A GLU 3.8 17.7 - - - +
306A LYS* 4.6 3.3 - - + +
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Residues in contact with GLN 116 (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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115A GLN* 1.3 86.6 + - - +
117A GLY* 1.3 59.0 + - - +
166A ALA* 3.4 12.5 - - - +
167A TRP* 3.6 42.3 - - + +
305A GLU 5.1 1.4 + - - -
403A 7S1 5.5 4.2 - - - -
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Residues in contact with GLY 117 (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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115A GLN 3.4 0.8 + - - -
116A GLN* 1.3 76.2 - - - +
118A LEU* 1.3 65.9 + - - -
165A SER* 3.4 3.8 + - - -
166A ALA 2.9 33.4 + - - +
168A CYS* 3.3 8.8 - - - -
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Residues in contact with LEU 118 (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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117A GLY* 1.3 74.7 - - - +
119A CYS* 1.3 64.8 + - - +
149A THR* 4.1 13.5 - - + -
163A GLU* 3.3 26.9 - - + +
164A VAL 3.2 4.5 - - - +
165A SER* 3.1 39.0 - - - +
168A CYS* 3.5 2.5 - - - +
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Residues in contact with CYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 1.3 72.5 - - - +
120A PRO* 1.3 75.3 - - + +
153A VAL* 4.9 0.7 - - - -
163A GLU* 4.6 4.6 - - - +
164A VAL* 2.9 41.5 + - - +
168A CYS* 2.0 53.2 - - + -
169A PRO* 4.2 11.9 - - + -
170A ILE* 4.2 18.2 - - - -
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Residues in contact with PRO 120 (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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119A CYS* 1.3 95.6 - - + +
121A ASP* 1.3 63.6 + - - +
122A PHE 3.8 0.5 + - - -
153A VAL* 3.3 32.1 - - + -
154A VAL 4.1 5.8 - - - +
155A TYR* 3.8 42.2 - - + +
161A THR* 3.4 13.7 - - - +
162A CYS 3.9 2.0 - - - +
164A VAL* 4.4 0.2 - - - -
170A ILE* 4.6 4.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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