Contacts of the strand formed by residues 71 - 83 (chain A) in PDB entry 4MXV
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 GLY 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A THR 3.8 2.2 + - - -
70A SER* 1.3 75.3 - - - +
72A ILE* 1.3 66.5 + - - -
73A TYR* 3.5 8.1 - - - -
140A GLN* 3.7 1.9 - - - -
141A LEU 3.0 32.7 + - - +
55D GLN* 5.4 2.7 - - - -
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Residues in contact with ILE 72 (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 GLY* 1.3 72.7 - - - -
73A TYR* 1.3 68.7 + - - +
138A ALA* 4.1 14.8 - - + -
139A PHE 3.4 5.4 - - - +
140A GLN* 3.1 37.2 - - + -
170A ALA* 3.7 1.9 - - - +
171A LEU* 3.0 57.1 + - + +
28D LYS 5.5 0.9 - - - +
30D ALA* 4.3 8.7 - - + -
53D PHE* 4.0 10.1 - - + -
55D GLN* 2.9 40.6 - - - +
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Residues in contact with TYR 73 (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 PRO* 4.5 2.8 - - + +
58A PHE* 3.7 29.2 - + - -
67A VAL* 3.4 19.5 - - + -
68A PRO* 3.3 16.1 - - + +
69A THR* 2.6 32.6 + - - -
70A SER 4.9 0.2 - - - -
71A GLY* 3.5 21.8 - - - -
72A ILE* 1.3 78.3 - - - +
74A PHE* 1.3 61.6 + - - +
75A VAL* 3.8 9.2 + - + -
137A ALA 3.5 0.9 - - - +
138A ALA* 3.2 3.4 - - - -
139A PHE* 2.7 39.4 + - - +
141A LEU* 3.8 28.5 - - + -
147A LEU* 6.3 0.4 - - + -
168A ALA* 4.9 1.6 - - + -
169A PHE* 3.2 23.1 - - - +
170A ALA* 3.7 19.7 - - + -
171A LEU* 4.5 3.4 - - - -
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Residues in contact with PHE 74 (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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73A TYR* 1.3 71.5 - - - +
75A VAL* 1.3 60.8 + - - +
76A TYR* 3.9 24.0 - + + -
134A TYR* 4.7 1.6 - - - -
136A GLY* 3.7 21.1 - - - -
137A ALA* 3.4 24.9 - - - -
138A ALA* 4.1 1.1 - - - +
167A GLY 4.1 0.2 - - - +
168A ALA* 3.2 4.3 - - - +
169A PHE* 3.0 69.5 + + + -
171A LEU* 4.2 10.0 - - + +
74B PHE* 4.1 18.8 - + - -
74D PHE* 3.8 31.4 - + - -
76D TYR* 4.2 4.0 - + - -
134D TYR* 4.0 4.0 - - - -
169D PHE* 3.4 21.5 - + + -
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Residues in contact with VAL 75 (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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73A TYR* 4.2 12.6 - - + -
74A PHE* 1.3 77.8 - - - +
76A TYR* 1.3 63.5 + - - +
101A VAL* 3.6 31.9 - - + -
114A LEU* 5.3 0.2 - - + -
115A LEU* 3.3 8.8 - - + +
136A GLY* 3.1 2.9 - - - -
137A ALA 2.9 28.2 + - - -
139A PHE* 3.9 24.0 - - + -
141A LEU* 4.4 4.3 - - + -
147A LEU* 3.8 29.8 - - + -
166A PHE* 4.3 7.4 - - + -
167A GLY 3.5 8.1 - - - +
168A ALA* 3.8 7.0 - - + -
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Residues in contact with TYR 76 (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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31A ALA 4.1 0.9 + - - -
32A HIS* 2.7 26.8 + - - +
74A PHE* 3.9 24.9 - + + -
75A VAL* 1.3 76.8 - - - +
77A SER* 1.3 63.2 + - - +
101A VAL* 4.9 0.9 - - - -
115A LEU* 4.6 0.4 - - - -
134A TYR* 3.7 17.7 - - - +
135A HIS 3.3 8.7 - - - +
136A GLY* 4.0 0.2 - - - -
165A PHE* 3.6 28.0 - + - -
166A PHE* 3.6 3.2 - - - -
167A GLY* 2.9 59.4 + - - +
168A ALA 3.8 2.5 - - - -
169A PHE* 4.2 18.6 - + - -
74B PHE* 4.7 1.3 - + - -
136B GLY 3.8 7.2 - - - -
137B ALA* 3.6 20.4 - - + -
138B ALA* 3.0 25.9 + - - +
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Residues in contact with SER 77 (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 TRP* 4.6 0.3 - - - -
76A TYR* 1.3 81.0 - - - +
78A GLN* 1.3 59.4 + - - +
99A HIS* 2.9 26.2 + - - -
101A VAL* 3.7 24.8 - - - +
133A MET 3.9 1.0 - - - +
134A TYR* 3.6 6.7 - - - -
135A HIS* 3.0 36.2 + - - +
149A THR* 4.5 0.4 - - - +
165A PHE* 2.7 22.8 + - - -
166A PHE* 3.9 9.7 - - - +
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Residues in contact with GLN 78 (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 TRP* 4.9 0.2 - - - -
77A SER* 1.3 78.4 + - - +
79A VAL* 1.3 74.6 - - - +
80A VAL* 4.2 4.6 - - - +
99A HIS* 4.6 0.9 - - - -
132A SER* 4.6 6.9 + - - +
133A MET 3.3 12.8 - - - +
134A TYR* 3.4 11.0 - - + +
162A SER 3.4 20.2 + - - -
163A THR* 3.1 21.5 + - - +
164A VAL* 3.3 2.8 - - - +
165A PHE* 2.8 54.9 + - + +
115B LEU* 5.8 0.2 - - - +
116B SER 4.1 11.3 + - - -
117B SER* 5.5 0.2 - - - -
134B TYR 4.4 0.2 - - - +
135B HIS* 3.1 34.9 + - - +
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Residues in contact with VAL 79 (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 LEU* 4.7 3.6 - - + -
78A GLN* 1.3 79.1 - - - +
80A VAL* 1.3 70.5 + - - +
81A PHE* 3.6 23.6 - - + -
99A HIS* 3.5 50.3 - - + +
132A SER* 3.6 1.4 + - - -
133A MET* 2.9 39.4 + - + +
151A THR* 4.8 1.8 - - + -
157A LEU* 3.7 22.4 - - + -
163A THR 3.7 0.4 - - - -
164A VAL* 3.6 13.5 - - + -
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Residues in contact with VAL 80 (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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78A GLN* 4.2 4.9 - - - +
79A VAL* 1.3 81.0 - - - +
81A PHE* 1.3 66.2 + - - +
130A LEU* 3.6 25.6 - - + -
131A HIS 3.5 9.6 - - - +
132A SER* 3.7 15.7 - - - +
157A LEU* 3.4 7.2 - - - +
158A VAL* 2.8 51.4 + - + -
163A THR* 3.4 33.0 - - + +
164A VAL* 3.6 5.1 - - - +
116B SER 5.1 3.4 - - - +
117B SER* 5.8 1.1 - - - +
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Residues in contact with PHE 81 (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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79A VAL* 3.6 26.9 - - + -
80A VAL* 1.3 75.3 - - - +
82A SER* 1.3 60.8 + - - +
97A LEU* 3.6 39.9 - - + -
98A ALA 4.0 4.5 - - - -
129A TRP* 3.6 6.1 - - + -
130A LEU* 3.2 10.0 - - - +
131A HIS* 2.7 40.1 + - + +
133A MET* 3.8 20.9 - - + -
151A THR* 3.9 16.2 - - + -
152A ASP 3.8 19.7 - - - -
153A GLY 3.4 28.3 - - - -
156A HIS 3.0 12.1 - - - +
157A LEU* 3.7 19.1 - - + -
158A VAL* 4.3 0.2 - - - -
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Residues in contact with SER 82 (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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81A PHE* 1.3 77.0 - - - +
83A GLY* 1.3 53.8 + - - +
129A TRP* 3.5 17.9 - - - -
130A LEU* 3.6 19.5 - - - -
156A HIS* 2.8 39.2 + - - +
157A LEU 5.5 0.3 - - - -
158A VAL* 3.8 13.3 - - - +
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Residues in contact with GLY 83 (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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82A SER* 1.3 76.7 - - - +
84A LYS* 1.3 69.6 + - - +
128A PRO* 3.3 9.5 - - - +
129A TRP* 3.1 44.3 + - - +
156A HIS* 4.0 7.4 - - - -
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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