Contacts of the strand formed by residues 6 - 18 (chain A) in PDB entry 4N41
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 LYS 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLY* 1.3 72.2 - - - -
7A THR* 1.3 68.7 + - - +
312A GLN* 3.3 27.7 - - - +
313A ALA 3.7 4.7 - - - +
314A TYR* 3.8 26.5 - - + -
315A ARG* 4.7 2.6 + - - -
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Residues in contact with THR 7 (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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6A LYS* 1.3 76.7 + - - +
8A GLU* 1.3 74.3 + - - +
9A VAL* 5.5 2.5 - - + -
312A GLN* 3.7 11.4 - - - -
313A ALA* 2.9 37.1 + - - +
315A ARG* 3.0 54.7 + - - +
583A PRO* 5.5 4.9 - - + -
585A GLN 5.3 7.6 - - - +
592A LEU* 5.5 4.4 - - + +
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Residues in contact with GLU 8 (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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7A THR* 1.3 85.5 - - - +
9A VAL* 1.3 73.2 + - - +
310A ARG* 3.2 45.2 + - + +
311A ALA 3.4 16.5 + - - +
312A GLN* 4.5 11.9 - - - +
583A PRO* 4.0 0.5 - - - +
584A VAL* 3.2 36.1 + - + +
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Residues in contact with VAL 9 (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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7A THR* 5.5 2.9 - - + -
8A GLU* 1.3 79.9 - - - +
10A PHE* 1.3 66.8 + - - +
11A LEU* 4.3 10.1 - - + -
310A ARG* 3.2 8.0 - - - +
311A ALA* 2.8 53.3 + - + +
313A ALA* 3.9 23.6 - - + -
581A VAL* 3.8 22.4 - - + -
582A TYR 3.1 17.3 - - - +
583A PRO* 4.4 2.9 - - + -
584A VAL* 4.0 7.0 - - - -
592A LEU* 4.2 11.2 - - + -
594A VAL* 4.4 6.1 - - + -
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Residues in contact with PHE 10 (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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9A VAL* 1.3 75.1 - - - +
11A LEU* 1.3 69.3 + - - +
287A ARG* 4.8 3.4 - - + -
291A ARG* 3.2 31.9 - - - +
308A ALA* 3.8 27.6 - - + -
309A VAL 3.5 2.7 - - - -
310A ARG* 3.6 53.4 - - + -
581A VAL* 3.5 5.4 - - - -
582A TYR* 2.8 41.8 + - + +
583A PRO 4.1 5.6 - - - -
584A VAL* 3.8 35.2 - - + -
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Residues in contact with LEU 11 (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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9A VAL* 4.3 11.2 - - + -
10A PHE* 1.3 85.3 - - - +
12A ASN* 1.3 62.0 + - - +
13A ARG* 3.1 48.5 + - + +
14A PHE* 5.1 2.3 - - - -
308A ALA* 5.1 2.8 - - - +
309A VAL* 3.0 31.2 + - + +
311A ALA* 4.4 12.8 - - + -
580A ARG 3.4 5.6 - - - +
581A VAL* 3.8 26.0 - - + -
582A TYR* 5.0 3.3 - - - -
594A VAL* 4.7 1.8 - - + -
596A LEU* 4.1 21.1 - - + -
602A LEU* 4.2 12.6 - - + -
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Residues in contact with ASN 12 (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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11A LEU* 1.3 71.5 - - - +
13A ARG* 1.3 59.0 + - - +
14A PHE* 3.4 13.4 - - - -
166A GLU* 3.7 17.1 + - - +
167A VAL 2.9 49.4 + - - +
168A ASP* 3.8 9.1 - - - +
290A THR* 4.0 13.2 - - + -
579A GLY* 3.7 6.8 - - - -
580A ARG* 2.9 51.9 + - + +
582A TYR* 4.4 5.8 - - + +
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Residues in contact with ARG 13 (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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11A LEU* 3.1 39.2 - - + +
12A ASN* 1.3 80.7 + - - +
14A PHE* 1.3 67.0 + - - +
156A TRP* 4.0 33.5 - - + -
164A LEU* 4.5 13.6 - - + +
165A LEU 3.0 14.4 - - - +
166A GLU* 4.6 9.2 + - + +
308A ALA* 3.5 1.9 - - - -
309A VAL* 2.9 47.0 + - + +
577A GLY 5.7 2.6 + - - -
578A GLY 5.9 2.8 + - - -
596A LEU* 5.1 17.0 - - - +
597A GLU* 5.5 4.2 + - - -
602A LEU* 6.3 0.8 - - - +
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Residues in contact with PHE 14 (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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11A LEU 5.1 1.6 - - - -
12A ASN* 3.4 23.8 - - - -
13A ARG* 1.3 80.3 - - - +
15A ALA* 1.3 62.7 + - - +
16A LEU* 3.6 0.7 + - - +
164A LEU* 3.5 7.9 - - - -
165A LEU* 2.8 42.6 + - + +
167A VAL* 4.1 8.7 - - + -
290A THR* 3.9 24.2 - - + -
291A ARG* 4.3 17.3 - - + -
294A ALA* 3.6 31.0 - - + -
306A PRO* 3.6 28.5 - - + -
307A GLU 3.3 6.3 - - - +
308A ALA* 3.5 33.2 - - + -
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Residues in contact with ALA 15 (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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14A PHE* 1.3 71.6 - - - +
16A LEU* 1.3 63.2 + - - +
162A ALA* 6.0 2.2 - - + -
163A PHE 3.8 6.3 - - - +
164A LEU* 4.1 9.4 - - + -
305A THR 3.5 3.8 - - - +
306A PRO* 3.4 4.9 - - - +
307A GLU* 2.7 45.5 + - + +
309A VAL* 4.0 6.5 - - + +
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Residues in contact with LEU 16 (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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14A PHE 4.4 3.4 - - - +
15A ALA* 1.3 78.5 - - - +
17A ARG* 1.3 67.9 + - - +
18A PRO* 3.7 1.9 - - - +
155A LEU* 4.3 15.7 - - + -
162A ALA* 3.8 8.7 - - - +
163A PHE* 3.0 25.2 + - + +
165A LEU* 4.1 24.5 - - + +
298A GLY* 5.4 1.8 - - - -
301A LEU* 4.3 13.5 - - + -
303A LEU* 3.4 24.7 - - + +
304A GLY* 3.4 27.8 - - - +
305A THR 3.8 1.8 - - - -
306A PRO* 3.5 29.6 - - + -
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Residues in contact with ARG 17 (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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16A LEU* 1.3 77.2 - - - +
18A PRO* 1.3 93.4 + - + +
19A LEU* 3.8 1.0 - - - +
20A ASN* 3.5 19.1 - - - +
23A GLU* 2.5 44.6 + - - -
162A ALA* 4.2 0.2 - - - -
163A PHE* 3.2 28.8 + - + -
302A GLY 4.7 3.6 + - - -
303A LEU* 3.0 48.8 + - - +
304A GLY* 4.9 4.8 - - - -
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Residues in contact with PRO 18 (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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16A LEU 3.7 2.0 - - - +
17A ARG* 1.3 110.3 + - + +
19A LEU* 1.3 66.4 + - - +
20A ASN* 3.6 0.3 + - - -
160A SER 5.3 2.9 - - - +
161A GLY 3.3 14.1 - - - +
162A ALA* 3.7 11.0 - - + -
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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