Contacts of the strand formed by residues 62 - 76 (chain A) in PDB entry 4LL4
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 GLN 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A MET* 3.4 25.6 - - + +
61A GLN* 1.3 84.8 + - - +
63A CYS* 1.3 60.3 + - - +
64A LYS* 5.4 1.3 - - - -
298A SER 3.3 19.4 - - - +
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Residues in contact with CYS 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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55A LEU* 3.3 2.1 - - - +
56A TRP* 2.8 69.8 + - + +
57A MET* 4.7 1.0 - - - +
58A GLN 5.0 0.2 - - - +
61A GLN* 4.2 4.3 - - - +
62A GLN* 1.3 75.2 - - - +
64A LYS* 1.3 63.1 + - - +
190A CYS* 2.0 57.4 - - - -
297A GLY 4.0 9.2 - - - -
298A SER 4.1 4.0 - - - -
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Residues in contact with LYS 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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53A LYS* 3.5 42.3 - - + +
54A VAL 3.3 15.0 - - - +
55A LEU* 3.6 16.6 - - + -
56A TRP* 4.9 0.9 - - - -
62A GLN 5.4 0.7 - - - -
63A CYS* 1.3 76.4 - - - +
65A GLN* 1.3 65.3 + - - +
66A THR* 3.8 17.4 + - - -
297A GLY* 3.3 6.8 - - - -
298A SER* 2.9 38.7 + - - +
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Residues in contact with GLN 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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52A ALA 4.2 0.2 - - - +
53A LYS* 3.6 1.2 - - - -
54A VAL* 2.8 48.4 + - + +
56A TRP* 5.0 1.2 - - - -
64A LYS* 1.3 73.2 - - - +
66A THR* 1.3 64.5 + - - +
67A SER* 3.6 20.0 + - - +
272A VAL* 3.5 24.9 + - - +
274A TYR* 3.7 13.0 - - - -
294A LEU 4.9 0.9 - - - +
295A VAL* 3.3 36.9 - - + +
296A ILE 3.4 29.7 + - - +
297A GLY* 3.8 3.1 - - - +
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Residues in contact with THR 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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51A VAL* 3.8 23.3 - - + -
52A ALA 3.7 4.0 - - - +
53A LYS* 4.5 7.6 - - + +
64A LYS* 3.8 24.4 + - - +
65A GLN* 1.3 78.4 + - - +
67A SER* 1.3 67.4 + - - +
68A GLU* 5.6 3.8 - - + -
270A LEU 4.7 2.6 - - - +
271A ARG* 5.2 2.4 - - - -
272A VAL 5.7 0.3 + - - -
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Residues in contact with SER 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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51A VAL* 3.7 1.7 - - - -
52A ALA* 2.9 38.8 + - - -
54A VAL* 6.0 1.0 - - - +
65A GLN* 3.6 23.4 + - - +
66A THR* 1.3 78.8 + - - +
68A GLU* 1.3 61.5 + - - +
69A TYR* 3.2 22.6 + - - -
270A LEU 4.1 1.1 - - - -
271A ARG* 3.5 24.5 - - - +
272A VAL 5.2 1.2 + - - -
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Residues in contact with GLU 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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50A GLY 3.4 9.4 - - - +
51A VAL* 4.0 18.6 - - + +
66A THR* 5.6 4.3 - - + -
67A SER* 1.3 71.5 - - - +
69A TYR* 1.3 72.7 + - - +
70A LEU 4.5 4.7 - - - +
71A ARG* 2.7 54.7 + - - +
269A ILE 4.8 0.7 - - - -
270A LEU* 3.1 41.3 + - + +
271A ARG* 3.1 19.1 + - - -
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Residues in contact with TYR 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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50A GLY 3.1 5.9 + - - +
52A ALA* 4.4 11.6 - - + +
67A SER* 3.2 30.7 - - - -
68A GLU* 1.3 88.2 - - - +
70A LEU* 1.3 64.2 + - - +
106A PRO* 3.3 27.4 - - + +
109A PRO* 3.2 38.6 - - + +
110A LEU* 3.8 14.6 - - + -
111A GLY* 3.8 24.8 - - - -
113A SER* 5.7 0.3 + - - -
123A TYR* 3.6 19.3 - - + +
270A LEU* 4.8 7.4 - - - -
271A ARG* 3.6 42.0 + - - +
273A GLU* 5.2 2.4 + - - +
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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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48A ALA* 3.9 14.6 - - + +
49A CYS* 3.4 9.8 - - - +
50A GLY* 3.3 29.4 + - - +
51A VAL* 5.7 0.2 - - - +
68A GLU* 4.5 3.8 - - - +
69A TYR* 1.3 86.2 + - - +
71A ARG* 1.3 68.1 + - - +
72A TYR* 4.5 13.9 - - + -
103A PHE* 3.7 31.4 - - + -
104A GLU 5.1 2.7 - - - +
105A LEU* 3.8 23.6 - - + -
106A PRO* 4.0 16.6 - - + -
123A TYR* 4.4 3.4 - - + -
143A PHE* 4.3 10.3 - - + -
270A LEU* 4.7 3.8 - - - +
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Residues in contact with ARG 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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47A LEU* 5.1 7.2 - - + -
48A ALA 3.7 3.6 - - - -
49A CYS* 5.3 7.0 - - - -
68A GLU* 2.7 42.9 + - - +
70A LEU* 1.3 76.2 - - - +
72A TYR* 1.3 60.9 + - - +
73A GLU* 5.4 5.8 - - - +
222A LEU* 3.8 31.6 - - + +
268A ASN* 3.7 40.2 + - - +
269A ILE 4.3 8.8 + - - -
270A LEU* 4.5 5.7 - - + +
224C ASN 5.1 2.7 - - - +
225C GLY 5.2 0.9 + - - -
226C GLN* 3.8 11.6 - - - +
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Residues in contact with TYR 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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46A ILE* 3.9 25.1 - - + +
47A LEU* 3.2 9.8 - - - +
48A ALA* 2.8 44.1 + - + +
70A LEU* 4.5 13.7 - - + -
71A ARG* 1.3 75.3 - - - +
73A GLU* 1.3 61.9 + - - +
74A ASP* 3.8 29.9 + - + +
102A GLY 3.3 16.8 + - - -
103A PHE* 3.6 38.6 - + + -
226C GLN* 3.4 25.1 - - - -
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Residues in contact with GLU 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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46A ILE 3.1 12.6 - - - +
47A LEU* 3.9 19.3 - - + +
71A ARG* 5.4 5.6 - - + +
72A TYR* 1.3 80.5 - - - +
74A ASP* 1.3 65.3 + - - +
224C ASN 4.3 11.4 - - - +
226C GLN* 2.8 24.2 + - - +
228C LYS* 3.0 42.8 - - - +
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Residues in contact with ASP 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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45A ARG* 3.4 4.7 - - - +
46A ILE* 2.8 39.8 + - + +
72A TYR* 3.8 28.9 + - + +
73A GLU* 1.3 78.2 - - - +
75A THR* 1.3 72.6 + - - +
76A LEU* 3.4 18.9 + - + +
101A PHE* 5.9 0.2 - - - -
102A GLY 6.0 0.2 + - - -
226C GLN* 5.8 0.2 + - - -
228C LYS* 4.1 11.8 - - - +
229C VAL* 5.2 9.9 + - - +
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Residues in contact with THR 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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43A ALA* 4.6 16.8 - - + -
44A VAL 3.8 12.3 - - - +
45A ARG* 4.1 13.5 - - + +
74A ASP* 1.3 91.2 + - - +
76A LEU* 1.3 67.3 + - - +
77A LEU* 4.4 9.8 - - + +
85A GLU* 4.3 33.0 + - + +
228C LYS* 5.7 1.7 + - - -
229C VAL 5.8 1.5 - - - +
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Residues in contact with LEU 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 VAL* 4.1 14.8 - - + -
44A VAL* 3.1 22.5 + - + +
46A ILE* 3.6 29.6 - - + -
74A ASP* 3.4 33.0 - - + +
75A THR* 1.3 74.6 - - - +
77A LEU* 1.3 74.0 + - - +
99A TYR* 3.7 31.8 - - + -
100A LYS 3.5 28.5 - - - +
101A PHE* 3.7 18.2 - - + -
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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