Contacts of the strand formed by residues 117 - 129 (chain A) in PDB entry 4U9W
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 VAL 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A TRP* 3.3 4.8 - - - -
113A GLU* 2.6 47.9 + - + +
114A ASN* 3.2 15.9 + - + +
116A SER* 1.3 90.9 - - - +
118A PRO* 1.3 72.7 - - + +
119A VAL* 4.5 8.1 - - + -
145A LYS* 5.6 2.2 - - - +
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Residues in contact with PRO 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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69A THR* 5.2 3.1 - - + +
72A TRP* 3.4 61.2 + - + +
110A ILE* 4.2 5.6 - - + -
111A ALA 3.3 8.1 - - - +
112A TRP* 3.4 27.3 - - + -
116A SER 3.5 9.2 - - - +
117A VAL* 1.3 91.7 - - + +
119A VAL* 1.3 61.1 + - - +
143A GLU* 4.2 3.6 - - - +
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Residues in contact with VAL 119 (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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55A VAL* 3.8 24.9 - - + -
72A TRP* 3.6 6.1 - - - -
111A ALA* 2.8 21.1 + - + +
113A GLU* 3.6 39.7 - - + +
117A VAL* 3.9 6.5 - - + +
118A PRO* 1.3 79.3 - - - +
120A ALA* 1.3 66.3 + - + +
143A GLU* 2.9 39.2 + - + +
145A LYS* 4.7 4.3 - - + +
146A VAL* 3.7 24.5 - - + +
151A LEU* 4.6 1.8 - - + -
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Residues in contact with ALA 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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72A TRP* 3.5 10.4 - - - -
110A ILE* 3.5 0.7 - - - -
111A ALA* 2.7 35.4 + - + -
119A VAL* 1.3 85.7 - - - +
121A PHE* 1.3 61.7 - - - +
141A GLN 3.3 6.5 - - - -
142A LEU* 3.5 30.5 - - + -
151A LEU* 3.9 19.3 - - + -
155A LEU* 4.3 5.4 - - + -
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Residues in contact with PHE 121 (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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72A TRP* 3.8 28.0 - + + -
73A ALA* 3.6 24.0 - - + -
76A LEU* 4.3 3.8 - - + -
77A THR* 3.1 20.9 - - - -
101A MET* 3.7 13.2 - - + -
108A TYR* 3.6 22.7 - + + -
109A LEU 3.0 15.7 - - - +
110A ILE* 4.3 8.1 - - + -
120A ALA* 1.3 74.6 - - - +
122A SER* 1.3 70.3 + - - +
123A HIS* 3.9 1.6 - - + -
139A GLU* 3.7 22.0 - - + -
140A VAL* 3.5 3.8 - - - +
141A GLN* 2.8 60.4 + - + -
155A LEU* 4.8 7.6 - - - -
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Residues in contact with SER 122 (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 TRP 3.5 0.7 - - - +
108A TYR* 3.3 8.1 - - - -
109A LEU* 2.9 47.9 + - - +
121A PHE* 1.3 80.0 - - - +
123A HIS* 1.3 63.5 + - - +
124A PHE* 3.9 3.9 + - - -
137A CYS* 3.8 2.6 - - - -
139A GLU 3.0 16.4 + - - -
140A VAL* 4.5 10.1 - - - -
155A LEU* 5.1 5.1 - - - +
159A LEU* 3.7 23.3 - - - +
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Residues in contact with HIS 123 (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* 3.5 28.4 + - + +
101A MET* 4.1 14.9 - - + +
106A ALA* 3.4 20.7 - - + +
107A TRP 3.4 5.8 - - - -
108A TYR* 4.0 20.6 - + + +
121A PHE* 3.7 4.1 - - + -
122A SER* 1.3 72.3 - - - +
124A PHE* 1.3 65.7 + - - +
125A ARG* 3.1 26.3 + - - +
137A CYS* 3.6 0.7 - - - -
138A TYR* 2.6 59.9 + + + +
139A GLU* 3.0 26.4 + - + +
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Residues in contact with PHE 124 (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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38A PRO* 5.3 0.4 - - + -
59A CYS* 3.9 18.6 - - - -
107A TRP* 2.9 69.0 + + + +
108A TYR 4.1 1.1 - - - -
109A LEU* 4.0 20.2 - - + -
122A SER* 4.1 11.4 - - - +
123A HIS* 1.3 75.4 - - - +
125A ARG* 1.3 71.7 + - - +
126A PHE* 3.7 28.7 - + - -
135A LEU* 3.7 26.9 - - + -
136A TYR 3.1 12.3 - - - +
137A CYS* 4.1 4.3 - - - -
138A TYR 4.2 0.2 - - - +
159A LEU* 3.6 21.8 - - + -
162A MET* 4.0 14.1 - - - -
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Residues in contact with ARG 125 (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* 2.6 42.6 + - - +
103A ASP* 3.3 19.1 + - - +
105A ARG* 3.4 55.3 - - + +
106A ALA* 4.1 3.4 - - - +
107A TRP* 4.5 1.6 - - - -
123A HIS* 3.1 19.8 + - - +
124A PHE* 1.3 84.3 - - - +
126A PHE* 1.3 69.6 + - - +
127A ASP* 4.0 8.8 + - + -
135A LEU* 3.4 7.3 - - - +
136A TYR* 2.8 32.6 + - + +
138A TYR* 3.4 38.0 + - + -
3F ARG* 5.1 2.3 - - - +
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Residues in contact with PHE 126 (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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29A VAL* 3.4 8.1 - - + +
32A ALA* 3.5 33.9 - - + -
33A ASN* 3.0 43.1 + - - +
38A PRO* 4.6 12.6 - - + -
105A ARG* 6.1 0.9 - - - +
107A TRP* 3.8 16.6 - + - -
124A PHE* 3.7 26.7 - + - -
125A ARG* 1.3 73.1 - - - +
127A ASP* 1.3 63.0 + - - +
134A VAL 3.6 2.0 - - - -
135A LEU* 3.7 24.5 - - + -
162A MET* 4.6 7.6 - - + -
166A THR* 3.4 31.4 - - + -
168A MET* 3.8 21.1 - - + -
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Residues in contact with ASP 127 (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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29A VAL* 3.6 12.1 - - - +
105A ARG* 5.3 11.8 + - - -
125A ARG* 4.0 10.8 + - + +
126A PHE* 1.3 77.3 - - - +
128A VAL* 1.3 83.0 + - - +
132A ASP 3.4 0.5 - - - +
133A GLU* 3.6 3.5 - - - -
134A VAL* 2.9 39.4 + - + +
136A TYR* 5.3 2.0 - - + -
3F ARG* 2.5 38.2 + - - +
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Residues in contact with VAL 128 (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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25A VAL* 3.9 23.3 - - + +
26A CYS* 5.2 10.3 - - - -
29A VAL* 4.1 13.5 - - + -
127A ASP* 1.3 90.3 + - - +
129A GLU* 1.3 65.9 + - - +
130A CYS 4.3 0.4 - - - +
131A GLY* 3.7 33.2 - - - +
132A ASP 3.1 3.8 - - - +
3F ARG* 3.7 11.4 + - - -
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Residues in contact with GLU 129 (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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127A ASP 3.9 0.2 + - - -
128A VAL* 1.3 76.2 - - - +
130A CYS* 1.3 91.1 + - + +
131A GLY 3.1 0.4 - - - -
132A ASP* 2.8 26.2 + - - +
134A VAL* 3.8 21.7 - - + +
136A TYR* 4.6 2.7 - - + -
172A MET* 3.6 30.1 - - + +
197A SER* 5.0 2.8 + - - -
3F ARG* 2.5 41.9 + - - +
5F LYS* 5.8 5.5 - - - -
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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