Contacts of the strand formed by residues 127 - 141 (chain A) in PDB entry 5UV6
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 ARG 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ASP* 3.7 18.4 - - - +
71A ARG* 4.7 7.1 + - - +
112A PRO* 4.0 30.1 + - + +
113A TYR 3.7 4.7 - - - +
114A THR* 2.6 38.9 + - + +
125A THR* 6.0 0.7 - - - +
126A SER* 1.3 76.7 + - - +
128A VAL* 1.3 68.3 + - - +
129A HIS* 4.8 15.7 - - + +
71B ARG* 5.6 2.2 - - - +
72B SER* 3.0 23.4 + - - +
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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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42A MET 5.2 3.6 - - - +
43A ASP* 3.3 19.7 - - - +
45A VAL* 3.5 32.3 - - + -
55A LEU* 5.4 8.1 - - + -
56A ARG 5.6 4.5 - - - +
68A TRP* 4.8 15.5 - - + -
112A PRO* 3.5 4.3 - - - +
113A TYR* 2.9 38.4 + - + +
126A SER* 3.8 8.3 + - - +
127A ARG* 1.3 78.5 - - - +
129A HIS* 1.3 71.2 + - - +
130A LEU 4.0 0.7 - - - +
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Residues in contact with HIS 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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43A ASP* 2.8 19.3 + - + -
44A ASN* 3.4 27.7 - - + +
45A VAL 2.7 32.4 + - - +
111A GLY* 3.6 4.8 + - - -
112A PRO* 4.1 27.3 - - + +
127A ARG* 4.8 15.2 - - + -
128A VAL* 1.3 79.4 - - - +
130A LEU* 1.3 59.4 + - - +
131A ILE* 3.6 8.0 + - + +
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Residues in contact with LEU 130 (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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45A VAL* 3.4 21.1 - - + +
47A VAL* 3.7 24.5 - - + -
53A ALA* 3.7 12.3 - - + -
55A LEU* 4.7 6.7 - - + -
102A ILE* 4.3 10.8 - - + -
105A VAL* 4.1 11.9 - - + -
109A ASP* 3.5 37.5 - - + +
110A GLU* 3.1 9.2 - - - +
111A GLY* 2.9 36.5 + - - +
113A TYR* 3.7 21.7 - - + +
128A VAL* 4.0 1.8 + - - +
129A HIS* 1.3 71.0 - - - +
131A ILE* 1.3 61.7 + - - +
132A VAL* 4.4 6.5 - - + -
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Residues in contact with ILE 131 (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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44A ASN* 3.6 37.9 - - + +
45A VAL 2.8 11.8 + - - +
46A THR* 3.3 22.5 - - + +
47A VAL* 3.0 27.2 + - - +
110A GLU* 3.7 13.5 - - + +
129A HIS* 4.2 8.7 - - + +
130A LEU* 1.3 76.3 - - - +
132A VAL* 1.3 67.6 + - - +
133A GLN* 4.9 4.7 - - + +
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Residues in contact with VAL 132 (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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47A VAL* 3.6 4.5 - - + +
49A GLN* 3.8 31.2 - - + -
105A VAL* 3.7 16.6 - - + -
106A ASP 3.3 28.3 - - - +
107A VAL* 3.9 19.5 - - + +
110A GLU* 2.7 42.5 + - + +
130A LEU* 4.4 6.1 - - + -
131A ILE* 1.3 77.0 - - - +
133A GLN* 1.3 65.5 + - - +
162A ARG* 3.5 17.8 + - - +
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Residues in contact with GLN 133 (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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46A THR* 3.4 29.7 - - + +
47A VAL 3.1 13.3 + - - +
48A ARG* 3.7 13.0 + - - +
49A GLN* 2.9 27.4 + - - +
131A ILE* 4.9 5.1 - - + +
132A VAL* 1.3 76.1 - - - +
134A VAL* 1.3 61.4 + - - +
135A PRO* 4.2 0.6 - - - +
162A ARG 3.3 17.3 - - - +
163A PRO* 4.3 12.9 - - + +
208A VAL* 4.5 23.6 - - + +
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Residues in contact with VAL 134 (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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49A GLN* 3.4 31.6 - - + +
107A VAL* 3.7 18.4 - - + -
132A VAL* 4.7 1.3 - - + -
133A GLN* 1.3 77.3 - - - +
135A PRO* 1.3 85.6 - - + +
137A GLN* 6.2 2.0 - - - +
160A ILE* 5.1 9.4 - - + -
161A GLY* 4.6 3.6 - - - -
162A ARG* 3.1 37.4 + - + +
206A ASN* 3.0 19.8 + - - -
208A VAL* 4.0 2.6 - - - +
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Residues in contact with PRO 135 (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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48A ARG* 3.4 31.2 - - - +
49A GLN* 5.4 5.2 - - + +
133A GLN 4.2 3.4 - - - +
134A VAL* 1.3 105.4 - - + +
136A PRO* 1.3 77.2 - - + +
137A GLN* 3.8 8.5 + - + +
160A ILE* 4.2 1.6 - - - +
161A GLY* 4.1 2.9 - - - -
208A VAL* 3.9 11.7 - - + -
209A ALA* 3.8 17.7 - - + -
210A ALA 4.9 1.3 - - - +
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Residues in contact with PRO 136 (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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134A VAL 3.6 0.6 - - - -
135A PRO* 1.3 89.9 - - + +
137A GLN* 1.3 66.8 + - - +
160A ILE 3.2 12.8 - - - +
161A GLY* 4.3 2.0 - - - -
165A PRO* 4.0 19.7 - - + -
204A ALA* 3.2 30.7 - - + +
205A LEU* 4.0 5.4 - - - -
206A ASN* 3.2 21.7 - - - +
208A VAL 3.5 3.6 - - - +
210A ALA 3.5 23.2 - - - +
211A PRO* 4.1 0.9 - - + -
212A ASP* 3.6 11.5 - - - +
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Residues in contact with GLN 137 (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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134A VAL* 6.2 2.0 - - - +
135A PRO* 3.8 6.0 + - + +
136A PRO* 1.3 80.7 - - - +
138A ILE* 1.3 66.5 + - - +
139A MET* 3.4 26.3 + - + +
159A ALA* 3.2 6.0 - - - +
160A ILE* 3.0 37.9 + - + +
212A ASP* 3.4 12.3 - - - +
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Residues in contact with ILE 138 (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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137A GLN* 1.3 73.8 - - - +
139A MET* 1.3 73.9 + - - +
140A ASN 3.9 14.4 - - - +
141A ILE* 4.2 14.1 - - + -
157A CYS* 3.5 34.8 - - - -
158A LEU 3.8 2.9 - - - +
159A ALA* 3.6 6.5 - - + -
202A CYS* 3.8 4.9 - - - -
204A ALA* 3.5 30.3 - - + -
212A ASP* 2.7 35.8 + - - +
213A VAL 4.8 0.7 - - - -
214A ARG* 4.7 18.2 - - + -
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Residues in contact with MET 139 (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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137A GLN* 3.4 49.8 + - + +
138A ILE* 1.3 79.4 - - - +
140A ASN* 1.3 70.9 + - - +
141A ILE* 4.1 1.9 + - - +
158A LEU* 3.0 26.5 + - + +
159A ALA* 4.9 0.4 - - - -
160A ILE* 3.8 33.4 - - + +
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Residues in contact with ASN 140 (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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138A ILE* 3.9 2.9 - - - +
139A MET* 1.3 86.8 - - - +
141A ILE* 1.3 63.4 + - - +
156A LEU 4.2 1.1 - - - +
157A CYS* 4.3 0.2 - - - -
158A LEU* 3.3 53.1 + - + +
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Residues in contact with ILE 141 (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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138A ILE* 4.2 10.5 - - + -
139A MET 5.5 1.3 - - - +
140A ASN* 1.3 75.0 - - - +
142A SER* 1.3 76.9 + - - +
143A SER* 3.4 3.2 + - - -
156A LEU 3.2 20.0 - - - +
157A CYS* 3.6 22.0 - - + -
169A TRP* 3.5 28.3 - - + -
202A CYS* 4.3 2.9 - - + -
214A ARG* 4.3 24.9 - - + +
215A LYS 4.9 8.1 - - - +
216A VAL* 4.8 6.1 - - + -
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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