Contacts of the strand formed by residues 60 - 73 (chain A) in PDB entry 1MVM
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 TRP 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A LEU* 2.4 55.4 + - + +
57A GLY 3.6 10.1 + - - +
58A ASP* 2.5 43.2 + - + +
59A GLY* 1.3 74.5 - - - +
61A VAL* 1.3 57.5 + - - +
137A GLN* 4.6 20.0 - - - -
534A ARG* 5.3 7.9 - - + -
535A ALA* 3.6 18.2 - - - -
536A LYS* 3.5 36.7 - - + +
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Residues in contact with VAL 61 (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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53A TYR* 4.1 8.5 - - + -
54A ARG 3.2 9.0 - - - +
55A PHE* 3.3 29.4 - - + -
56A LEU* 3.9 1.8 - - - +
60A TRP* 1.3 76.8 - - - +
62A GLU* 1.3 66.3 + - - +
63A ILE* 3.7 22.4 - - + -
135A MET* 3.1 37.0 - - + -
534A ARG* 3.3 7.4 - - - +
535A ALA 2.7 35.2 + - - +
537A LEU* 3.5 16.6 - - + -
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Residues in contact with GLU 62 (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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52A HIS 3.7 4.7 - - - +
54A ARG* 2.9 57.8 + - + +
56A LEU* 3.5 19.1 - - + +
61A VAL* 1.3 78.5 - - - +
63A ILE* 1.3 63.0 - - - +
64A THR* 3.8 15.5 + - - +
141A VAL* 5.5 0.3 - - - +
532A THR* 5.7 5.2 - - - -
533A MET 3.5 9.4 - - - +
534A ARG* 2.3 49.0 + - + -
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Residues in contact with ILE 63 (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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51A THR* 4.8 10.8 - - + -
52A HIS 3.6 4.5 - - - +
53A TYR* 3.2 37.9 - - + -
61A VAL* 3.7 15.7 - - + -
62A GLU* 1.3 71.9 - - - +
64A THR* 1.3 65.2 + - - +
65A ALA* 4.7 2.9 - - + +
123A LEU* 5.0 10.1 - - + -
131A ILE* 4.6 13.5 - - + -
135A MET* 4.1 16.6 - - + -
138A LEU* 4.4 19.3 - - + -
531A LEU 3.8 1.6 - - - +
532A THR* 3.4 1.6 - - - -
533A MET* 2.7 61.0 + - + +
535A ALA* 4.6 3.1 - - + -
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Residues in contact with THR 64 (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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50A GLN 4.2 0.7 - - - +
51A THR* 3.8 0.9 - - - -
52A HIS* 2.9 48.8 + - + +
62A GLU* 3.8 16.7 + - - +
63A ILE* 1.3 73.4 - - - +
65A ALA* 1.3 59.6 + - - +
66A LEU* 4.1 21.6 + - + +
530A LYS* 4.5 10.3 - - + -
531A LEU 3.6 3.8 - - - +
532A THR* 4.3 21.3 - - + +
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Residues in contact with ALA 65 (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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50A GLN 3.9 4.3 - - - +
51A THR* 4.5 7.4 - - + +
63A ILE* 3.9 5.3 - - + -
64A THR* 1.3 74.5 - - - +
66A LEU* 1.3 68.2 + - - +
122A TRP* 3.4 38.5 - - + +
123A LEU* 4.6 8.5 - - + -
529A GLY 3.6 0.5 - - - +
531A LEU* 2.7 43.4 + - + +
533A MET* 5.2 4.3 - - + -
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Residues in contact with LEU 66 (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 ASP* 3.1 43.5 - - + +
49A ASN* 3.5 9.6 - - - +
50A GLN* 2.9 20.7 + - + +
51A THR* 5.3 0.7 + - - -
52A HIS* 4.3 19.7 - - + +
64A THR* 4.3 12.3 - - + +
65A ALA* 1.3 85.5 - - - +
67A ALA* 1.3 67.1 + - - +
121A VAL 4.9 1.2 - - - +
122A TRP* 4.6 6.0 - - - +
528A LYS* 4.7 8.1 - - - +
529A GLY 2.6 18.2 - - - +
530A LYS* 3.6 24.5 - - + -
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Residues in contact with ALA 67 (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 ASP 2.7 10.2 + - - -
49A ASN* 2.9 20.2 - - - +
66A LEU* 1.3 76.1 - - - +
68A THR* 1.3 58.9 + - - +
69A ARG* 3.8 9.2 - - - +
121A VAL 3.7 21.5 - - - +
122A TRP* 4.5 6.3 - - + -
527A TRP* 3.4 15.1 - - + -
528A LYS* 2.8 2.3 - - - -
529A GLY 2.4 37.4 + - - -
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Residues in contact with THR 68 (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 TYR* 2.4 78.2 + - - -
48A ASP 2.8 28.4 + - - +
49A ASN* 3.0 7.4 - - - +
67A ALA* 1.3 69.3 - - - +
69A ARG* 1.3 59.1 + - - +
148A PHE* 4.3 5.6 - - + -
526A PHE* 5.3 1.1 - - - -
527A TRP 2.5 15.0 - - - -
528A LYS* 2.9 34.8 - - + -
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Residues in contact with ARG 69 (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 TYR* 4.9 1.3 - - - -
49A ASN* 3.5 13.4 + - - +
67A ALA* 3.8 3.6 - - - +
68A THR* 1.3 74.4 - - - +
70A LEU* 1.3 57.4 + - - +
71A VAL* 3.8 0.7 + - - +
121A VAL* 3.0 46.3 + - - +
198A LEU* 4.1 15.7 - - + -
199A GLY* 2.9 31.6 + - - +
200A PHE 3.2 6.0 + - - -
201A TYR 4.3 0.6 + - - -
202A PRO* 3.0 56.1 - - + +
204A LYS 4.9 6.1 - - - +
206A THR* 3.4 24.2 - - + -
526A PHE* 3.6 1.2 - - - -
527A TRP* 2.5 57.3 + - + +
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Residues in contact with LEU 70 (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 TYR* 5.2 1.3 + - + -
68A THR 3.9 2.4 + - - -
69A ARG* 1.3 72.7 - - - +
71A VAL* 1.3 66.1 + - - +
72A HIS* 6.4 0.9 - - + -
202A PRO 5.8 0.6 + - - -
204A LYS 5.7 0.2 + - - -
205A PRO* 3.4 40.6 - - + +
206A THR* 3.3 23.7 + - - +
524A THR* 4.0 29.6 - - + -
525A PHE 3.6 3.6 - - - -
526A PHE* 3.8 48.7 - - + +
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Residues in contact with VAL 71 (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 ARG 4.1 7.0 - - - +
70A LEU* 1.3 82.9 - - - +
72A HIS* 1.3 72.4 + - - +
73A LEU* 4.9 1.1 - - + -
114A VAL* 5.7 3.8 - - + -
198A LEU* 4.0 26.9 - - + -
205A PRO* 6.1 0.2 - - - -
206A THR* 3.6 15.0 - - + +
207A ILE* 5.0 1.8 - - - +
208A ALA* 4.5 18.2 - - + +
523A GLY 3.8 1.0 - - - +
524A THR* 3.3 8.3 - - - -
525A PHE* 2.8 73.0 + - + +
527A TRP* 4.8 2.5 - - + -
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Residues in contact with HIS 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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70A LEU* 6.4 0.2 - - + -
71A VAL* 1.3 81.0 - - - +
73A LEU* 1.3 65.3 + - - +
74A ASN* 3.3 37.9 + - - -
205A PRO* 5.8 5.6 - - + -
206A THR 3.2 12.7 + - - +
207A ILE* 3.6 29.8 - - + +
208A ALA 4.2 2.6 + - - -
522A TYR* 3.8 25.1 - + - -
523A GLY 3.6 9.4 - - - -
524A THR* 4.6 12.6 - - + +
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Residues in contact with LEU 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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71A VAL* 4.9 2.7 - - + -
72A HIS* 1.3 78.5 - - - +
74A ASN* 1.3 86.9 - - - +
76A PRO* 5.6 1.8 - - + -
112A SER* 3.6 30.3 - - - +
176A MET* 4.2 7.9 - - + -
208A ALA* 5.6 4.7 - - + -
499A VAL* 3.5 30.7 - - + +
500A ARG* 3.9 3.1 - - - -
501A LEU* 3.9 33.5 - - + +
522A TYR* 3.9 1.4 - - - +
523A GLY 3.0 32.7 + - - +
525A PHE* 4.4 10.1 - - + -
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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